bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examination Of Retinoic Acid And Oct3/4 Relationship In Gonadal Development
Authors: Albayrak Merve , Tapul Leyla 
Published: December 2016

INTRODUCTION
Early developmentof the gonads is monitored in the same morphological appearance in both sexes. Retinoic acid, plays a role in the formation process of mammalian germ cells and is also effective in the selection of male or female identity (2). Oct3/4, which is a transcription factor, is expressed in blastula, morula, inner cell mass of blastocyst and then in the primordial germ cells (8). Retinoic acid has been reported to be one of the possible regulators of Oct3/4 expression (3,7). This study was planned to evaluate the effects of the exogenous retinoic acid on gonadal development in mouse embryos and Oct3/4 expression of primordial germ cells.

MATERIALS AND METHODS
In this study, we used 12 Balb/c pregnant mice. No drug was given to the control group. The experimental group of Balb/c mice were given by oral gavage a dose of 80 mg / kg of retinoic acid dissolved in a mixture of absolute ethyl alcohol‐corn oil (the days of 6.5, 7.5, 8.5). In the meantime, the second control group was formed and given by oral gavage only a suspension of absolute ethyl alcohol‐corn oil for 3 days. Total of 73 embryos 11.5 ‐ 12.5dpc from the control and experimental groups were evaluated.

RESULTS
In fetal gonads of the experimental group (Fig. 1and 2), a smaller number of primordial germ cells was marked with Oct 3/4 immunohistochemically compared to the first and second control groups.

DISCUSSION
A fine set of changes in the levels of retinoic acid are reported to control gonadal development at different stages of embryogenesis (1). Retinoic acid has been reported to have an important role in the sex differentiation of mouse gonads and shows its effect as a meiosis inducing factor (4,5). Suppression of Oct3/4 expression in primordial germ cells that reached and settled in the gonads, is a critical step in the process of embryogenesis. A retinoic acid sensitive element localized in the promoter‐enhancer region has been reported to play a role in suppression of Oct 3/4 in a study of embryonal carcinoma cells(6). The study concluded that, retinoic acid regulates the development and differentiation of primordial germ cells during embryogenesis by suppressing Oct 3/4 expression and the opinion to control this process externally by using activators or inhibitors of retinoic acid receptors, become stronger.
Structural insight into the function of full‐length human Fanconi Anemia
FANCD
2/
FANCI
complex by cryo‐electron microscopy
Authors: Li Zhuolun , Liang Chih‐Chao , Nicholson William , Cohn Martin , Venien‐Bryan Catherine 
Published: December 2016

INTRODUCTION
At the center of the DNA damage Fanconi Anemia repair pathway is the FANCD2/FANCI complex, which is monoubiquitinated upon DNA damage, and this monoubiquitination is indispensable for activation of the pathway. However, neither FANCD2 nor FANCI have any recognizable domains, which results in limited understanding of the molecular functions of the complex. In this study, we have taken a structural approach to better understand the function of the human FANCD2/FANCI complex.

RESULTS

Experimental methods
The native full‐length human FANCD2/FANCI complex and the FANCD2/FANCI complex with the C‐terminus FANCD2 truncated were purified and subjected to cryo‐EM analysis. The activity of the complex was studied
in vivo
and
in vitro
using various assays.

Results

Here, we provide the first structural insight into the full‐length human FANCD2/FANCI complex utilizing cryo‐EM. The complex has a pocket‐like main body, a thumb‐like structure consisting of the C‐terminus of FANCI and a distinctive fork‐like tower consisting of the C‐terminus of FANCD2 (figure). Deletion of the C‐terminus of FANCD2 leads to defective DNA interstrand cross‐link repair (ICL repair). FANCD2 lacking the C‐terminus cannot be monoubiquitunated, while the
bona fide
monoubiquitination site (Lysine 561) is still present. Furthermore, the association with FANCI and the interaction between FANCD2 and the responsible E3 ligase complex, the FA core complex, remain unaffected in the mutant. The structure of the FANCD2/FANCI complex with the C‐terminus FANCD2 truncated was also studied using cryo‐EM, this truncated domain is located in the fork‐like tower (Figure )

Conclusion

Conclusion
A new domain of FANCD2 was discovered. The fork‐like tower domain in the C‐terminus of FANCD2 is required for its complete functions in the ICL repair. Interestingly, several disease‐causing mutations lie within this region, underscoring the importance of this domain.

Translational applicability
Our results contribute to uncover the mechanism of how the FANCD2/FANCI complex functions. A better understanding of the molecular mechanism underlying the FA pathway will increase our chances of developing better and more targeted modes of treatment.

Reference

1‐ Liang CC, Zhan B, Yoshikawa Y, Haas W, Gygi SP and Cohn MA. UHRF1 Is a Sensor for DNA Interstrand Crosslinks and Recruits FANCD2 to Initiate the Fanconi Anemia Pathway.
Cell reports
10
, 1947‐1956, doi:10.1016/j.celrep.2015.02.053 (2015
Ultra‐High Resolution
SEM
for Materials Analysis
Authors: Jiruše Jaroslav , Havelka Miloslav , Polster Jan 
Published: December 2016

The need for increased SEM resolution and the simultaneous demand for enhanced analytical capability have led to the development of increasingly sophisticated instruments. Here we describe the design of a novel SEM column where recently‐developed high‐resolution optics [1] is brought together with traditional analytical capabilities. Combined with FIB it greatly enlarges the capability for 3D tomography inspection of a specimen especially when used in combination with other analytical techniques like EDS or EBSD.
The SEM column comprises a triple objective lens design. The first objective lens is optimized to yield an image resolution of less than 1.1 nm at 1 kV. The design retains a single‐pole lens [2] which creates a strong magnetic field around the sample, dramatically decreasing optical aberrations. However, the leaking magnetic field distorts ion trajectories of the FIB and causes beam splitting of ion‐isotopes. To overcome this, FIB processing is performed in a magnetic‐field‐free mode, where the second objective lens of a conventional type with a resolution of 2.5 nm is used. The third objective lens enables a large field of view. A combination of all three objective lenses allows for multiple display modes, e.g. for enlarged field of view, greater depth of field or optimizing resolution at high probe currents. To prevent thermal instability due to changes of lens excitation when switching between the imaging, analytical and other modes, the column works in a regime where constant thermal power dissipation is maintained independent of lens excitation. It significantly reduces image drift and enables stable, long‐term, automatic 3D analysis.
3D BSE tomography of an SERS‐active structure of gold‐coated, partially‐etched polystyrene spheres (Figure 1) was performed maintaining stable operation over a 13 hour period [3]. The sample was sliced using FIB and each cross‐section was automatically imaged at 2 kV using one of the three dedicated back‐scattered electrons (BSE) detectors to obtain the gold distribution on the polystyrene surface. InBeam BSE detector placed in the column acquires high‐angle BSE signal, whereas the two other detectors collect BSE with lower angles. The BSE detector triplet thus enables angle filtration. Furthermore, energy‐filtering of the BSE signal enhances material contrast, (Figure 2), where low‐loss 1.95‐2 keV BSEs reveal details not observable in the integral BSE signal.
The redesigned electron gun further enhances the analytical capabilities of the column. It allows probe currents as high as 400 nA for structural analysis and ten times faster beam energy alternation compared to the previous generation. The sharp conus of the objective pole‐piece enables FIB processing of large tilted samples, e.g. 8 inch wafers. The new SEM column will be used in the Mark II generation of the TESCAN MAIA electron microscope and the dual FIB‐SEM instruments GAIA and XEIA [4].
Correlation of interface morphology and composition in
GaInP/GaAs
with growth conditions
Authors: Han Han , Beyer Andreas , Belz Jürgen , König Alexander , Stolz Wolfgang , Volz Kerstin 
Published: December 2016

Ternary (GaIn)P materials ststems grown on GaAs have attracted a lot of attention for laser applications, especially due to the low recombination velocities at the interface [1]. The physical properties of the interface are greatly influenced by the interface morphology, which can be controlled by either the growth temperature or growth interruptions or the introduction of interlayers, consisting e.g. of GaP. The interface morphologies of the semiconductor quantum wells can be characterized by the quantitative evaluation of high resolution high angle annular dark field (HAADF) images in scanning transmission electron microscopy (STEM). In the present work, quantitative evaluation of HAADF imaging in STEM is used to correlate the interface morphology and composition in (GaIn)P grown on GaAs with the growth conditions.
The (GaIn)P/GaAs QWs were grown with metal organic vapor phase epitaxy (MOVPE) on GaAs (001) substrate at temperatures of 525°C and 625 °C, respectively, with different growth interruption times with or without GaP interlayer. In order to be able to compare different samples, a carefully applied method to gain reliable results from high resolution STEM micrographs was used. Also, to derive the chemical composition maps, the chemical sensitive background intensity is subtracted after image normalization as shown in Figure 1. From the composition maps, the interface features are revealed and then correlated with the growth conditions. The growth interruptions can significantly affect the composition fluctuation and the interface morphology. At higher temperature of 625 °C, with the two GaP monolayers between (GaIn)P and GaAs substrate, shorter growth interruption time leads to intermixing at the interface while a longer growth interruption results in a sharp interface. Also, without the GaP buffer layer, platelet islands can be observed at the interface. At lower temperature of 525 °C the GaP buffer layer has less influence. Hence, the quantitative evaluation of HAADF STEM images can reveal the interface morphologies, which also have important influence on the optoelectronic properties.
Electron microscopic characterization of thermally modified surface layers generated by electro‐discharge machining
Authors: Ehle Lisa , Schneider Sebastian , Schwedt Alexander , Richter Silvia , Mayer Joachim 
Published: December 2016

Functional properties of construction components like wear resistance or fatigue strength heavily depend on their surface modifications like grain size, residual stresses, hardness, etc. Since these modifications are generated during machining, knowing about the resulting modifications beforehand is in high demand in industry. So far many time‐consuming iterative procedures are necessary to find the machining parameters that provide the desired surface integrity. Brinksmeier et al. [1, 2] introduced a new energy based approach called “Process Signatures” that is supposed to solve this problem. Process Signatures describe the relationship between internal material loads – like strain, temperature and their gradients – and the resulting material modifications for instance residual stresses, hardness and microstructure. Hence production processes are characterized by their mechanical, thermal and chemical loads or a combination of those instead of their machining parameters. The present work focuses on electro discharge machining (EDM), which is mainly characterized by thermal effects due to the high temperatures and temperature gradients arising from the generated spark plasma [3, 4].
In the present studies, scanning electron microscopy (SEM), electron backscatter diffraction (EBSD), electron probe microanalysis (EPMA) and transmission electron microscopy (TEM) have been used to analyze the surface modification of 42CrMo4 steels processed by EDM. According to the very high surface temperatures (above melting temperature) and high temperature gradients applied by EDM, the surface zone contains martensite and even dendrites (figure 1). Investigations on the carbon content in the surface zone reveal about 8 times higher carbon contents than in the matrix due to carbonization (figure 2). Carbonization occurs because of decomposition of the dielectric fluid and carbon diffusion results due to the high applied temperatures. The increase in carbon content also stabilizes the fcc crystal structure, as the EBSD phase map shows (figure 3). These surface modifications reveal information about the mechanisms and applied internal loads, since the internal loads, in particular temperature and temperature gradients, influence diffusion of carbon, generation of dendrites and martensitic transformation. Together with temperature measurements during processing and simulation of temperature evolution in the material, Process Signatures for EDM can be developed.
Investigations of transition metal dichalcogenides with momentum‐resolved electron energy‐loss spectroscopy
Authors: Huang Michael R. S. , Wilfried Sigle , van Aken Peter A. 
Published: December 2016

Investigations of transition metal dichalcogenides with momentum‐resolved electron energy‐loss spectroscopy
Michael R. S. Huang, Wilfried Sigle, and Peter A. van Aken
Max Planck Institute for Solid State Research, Stuttgart, Germany
When fast electrons pass through a thin film, various solid‐state excitations occur through mutual Coulomb interactions, which convey useful information relevant to the fundamental materials properties. Measurements by momentum‐dependent electron energy‐loss spectroscopy (q‐dependent EELS or ω ‐ q map) directly access the dispersion relation, enabling the physical origins of the intrinsic electronic excitations to be explored [1]. This research is concentrated on anisotropic titanium diselenide (TiSe2), a two‐dimensional material in the transition metal dichalcogenide group. The ω ‐ q maps were acquired in the Zeiss sub‐electron‐volt‐sub‐angstrom microscope (SESAM), which is equipped with a monochromator and the advanced in‐column Mandoline energy filter. To enhance the angular resolution, the specimen was purposely raised above the eucentric height, which significantly extends the effective camera length (ECL) beyond the originally achievable specification [2]. Figure 1 shows the characteristic dispersion of TiSe2 recorded along the momentum transfer parallel to the Γ‐K direction. The specific selection of scattering vector in reciprocal space is achieved through a narrow slit well positioned in the filter entrance pupil plane. With further increase of the ECL as well as in the spectral magnification, the details of the dispersion become clearly resolved (Figure 2). Similar to other layer‐ structured crystals such as graphite or molybdenite (MoS2) [3,4], the two dominant features at approximately 6.5 and 19.7 eV can be interpreted as the π and π + σ plasmons, which stem from the collective oscillations of the π and π + σ valence electrons, respectively. Moreover, another weak spectral feature at a lower energy of about 1.9 eV without significant dispersive behavior was also noticed. This excitation could probably be attributed either to the interband transition or to another plasmon resonance as a result of the negative real part of the dielectric function within this regime. However, more comprehensive investigations are required for clarity.
Efficient motor neuron targeting in adult mice by a single lumbar intrathecal r
AAV
9‐e
GFP
administration: application for motor neuron diseases
Authors: Bey Karim , Deniaud Johan , Carine Ciron , Dubreil Laurence , Aubourg Patrick , Colle Marie‐Anne 
Published: December 2016

Spinal muscular atrophy (SMA) the second most common autosomal recessive disorder causes of childhood mortality affecting between 1/6000 to 1/10000 live births. SMA is due to deletion/mutations in the
Survival Motor Neuron 1
(SMN1) gene. The disease is characterized by degeneration of spinal motor neurons (MNs), atrophy of skeletal muscles, and generalized weakness. SMA is clinically classified into four main types (I, II, III and IV) based on the age of onset and clinical severity. Currently, no curative treatment exists for SMA type II/III SMA patients representing the majority currently awaiting treatment.

Gene therapy, restoring SMN1 activity in MNs, is a promising therapeutic strategy for SMA. In the moderate forms (type II/III) of the disease, no lesion is found in peripheral organs. Thus, a targeted therapy directly into the CNS should be more appropriate. We have, recently, demonstrated that a single administration of an rAAV9 vector into the cerebrospinal fluid leads to an efficient transduction of MNs in non‐human primates.

In order to treat our mouse model that can mimick the human pathology of type II/III SMA, the first main challenge was to develop an efficient and safety route of delivery that can target whole spinal cord and brain. In this context, we develop the lumbar intrathecal delivery (itlumb), by single percutaneous lumbar puncture. We demonstrate that a single lumbar intrathecal injection of rAAV9‐eGFP vector using specific neuronal promoter can efficiently and specifically target MNs from proximal to distal part of the spinal cord in adult mice, wherease, using rAAV9‐eGFP ubiquitous promoter, we observe both glial cells and MNs targeting
(figure a, b and c)
. Surprisingly, by lumbar administration, we efficiently reach the brain and target neurons and glial cells using rAAV9 ubiquitous promoter
(figure g)
.

Then, we compared the serotypes 9 and 10 of AAV vector in order to demonstrate which serotype is the most efficient to target MNs after intrathecal delivery. We used the Synapsin 1 (SYN1) promoter, that lead to specific expression in neuron cells population, in adult mice, by lumbar intrathecal administration. We observed a spectacular and specific MNs expression with the serotype 9 around 50% and 10 % in the lumbar and cervical spinal cord respectively. Wherease the serotype 10 transduce less significantly MNs cells (30% and 5 % in the lumbar and cervical spinal cord respectively).
This results, offer new perspectives for the treatment of motor neuron diseases such as moderate forms of spinal muscular atrophy.
Improving
3d
correlation in integrated correlated light and electron microscopy using confocal laser scanning microscopy
Authors: Sueters‐Di Meo Josey , Kruit Pieter , Hoogenboom Jacob 
Published: December 2016

In CLEM experiments biological samples are typically first investigated by light microscopy (LM) to locate a region of interest. Next, nanometer‐scale imaging can be achieved by electron microscopy (EM). This results in identification of biomolecules within the ultrastructure and/or the possibility to correlate ultrastructure with preliminary live‐cell dynamics on biomolecules [1].
We have developed an integrated CLEM with which widefield fluorescence microscopy (WF‐FM) and EM can be performed in principle simultaneously [2]. Integration of these two modalities allows for fast ROI retrieval [3], optional fast switching between modalities increasing CLEM throughput, high (5 nm) correlation accuracy for the overlay [4], and novel imaging applications [5]. However, for WF‐FM the depth correlation for thick specimen or live cells contained in a dedicated liquids sample holder [6] is relatively poor. WF‐FM images through the entire sample and SEM only the upper ~100 nm (depending on e‐beam energy). We therefore integrated a Confocal Laser Scanning Microscope (CLSM) into a scanning electron microscope (SEM) via a Delmic Secom stage (Fig. 1‐4). This system will allow imaging with improved depth‐correlation by suppression of out‐of‐focus light contributions and will provide 3D optical information in CLEM.
We present our integrated CLSM SEM, using a commercial confocal scanner unit. We also demonstrate the procedure for alignment of the CLSM and SEM axes, needed to image the same area with both modalities. Lastly, the results of proof‐of‐principle experiments are presented, showing optical sectioning in thick specimen such as resin blocks or whole cells for improved LM‐SEM correlation along the axial direction.
TEMinvestigation of the effects of cycling on electrochemically stable hybridPt@NbOxnanocatalysts
Authors: Chinchilla Lidia , Rossouw David , Trefz Tyler , Kremliakova Natalia , Botton Gianluigi 
Published: December 2016

Renewable energies and fuel cell technologies will likely play a major role in reducing our dependency on fossil fuels. In particular, proton exchange membrane fuel cells (PEMFCs) are suitable for use in both domestic and automotive applications. This sophisticated technology requires a functional nanostructured material that contains platinum to catalyse both the hydrogen oxidation reaction (HOR) and the oxygen reduction reaction (ORR) to produce water, electricity, and heat. [1] Unfortunately, in spite of their remarkable potential, the high cost and degradation of platinum‐based catalytic materials have been a barrier to widespread adoption of this type of technology. Reducing platinum content while simultaneously improving the durability will therefore require novel approaches in the catalyst design and its characterization at nanoscale level. [2]Transmission Electron Microscopy (TEM) techniques have continued to play a major role in the design and characterization of PEMFC materials. Using an aberration‐corrected microscope (Titan cubed 80‐300), we investigated the structural stability over the lifetime of a proposed fuel cell cathode material containing nano‐particulate platinum on a NbOx‐carbon hybrid support. The characterization of this material included a series of ex‐situ TEM analyses before or after accelerated stress tests that cycled the sample 30,000 times between 0.6 and 1.0 V in an electrochemical cell.The histograms shown in Fig1a and b reveal that some metal particle coarsening occurred during the 30,000‐cycle test. The as‐prepared catalyst contained 1–5 nm particles, the majority of which were determined to be bimetallic, as determined by electron energy loss spectroscopy (EELS), with some Pt‐rich particles and Nb‐rich grains (Fig. 1c). After 30,000 cycles, microanalysis data confirms that the cycling treatment caused some agglomeration of the small Pt‐rich particles. Analysis of the EELS oxygen K ionization edge indicates that multiple niobium oxidation states are present in the system, predominantly Nb(V) before electrochemical cycling (Fig 1c). Although conventional image comparisons between the initial and final state of the hybrid catalyst suggest that the Pt particle size increased marginally, in order to obtain an improved understanding of the material's degradation, morphological and structural evolution of the particles and hybrid support were tracked using the so‐called Identical Location TEM technique [3]. The results in figure 2 indicate that no large‐scale degradation of the hybrid support took place, suggesting carbon corrosion was minimized. In addition, only minor changes occurred to the average particle size, demonstrating the excellent stability of the metallic particles. These findings demonstrate that highly dispersed Pt/NbOxon carbon support material is a promising electrocatalyst for PEMFC.