A Bioinformatically Initiated Approach to Evaluate GATA1 Regulatory Regions in Samples with Weak D, Del, or D- Phenotypes Despite Normal RHD Exons.

Introduction: With over 360 blood group antigens in systems recognized, there are antigens, such as RhD, which demonstrate a quantitative reduction in antigen expression due to nucleotide variants in the non-coding region of the gene that result in aberrant splicing or a regulatory mechanism. This study aimed to evaluate bioinformatically predicted GATA1-binding regulatory motifs in the RHD gene for samples presenting with weak or apparently negative RhD antigen expression but showing normal RHD exons. Methods: Publicly available open chromatin region data were overlayed with GATA1 motif candidates in RHD. Genomic DNA from weak D, Del or D- samples with normal RHD exons (n = 13) was used to confirm RHD zygosity by quantitative PCR. Then, RHD promoter, intron 1, and intron 2 regions were amplified for Sanger sequencing to detect potential disruptions in the GATA1 motif candidates. Electrophoretic mobility shift assay (EMSA) was performed to assess GATA1-binding. Luciferase assays were used to assess transcriptional activity. Results: Bioinformatic analysis identified five of six GATA1 motif candidates in the promoter, intron 1 and intron 2 for investigation in the samples. Luciferase assays showed an enhancement in transcription for GATA1 motifs in intron 1 and for intron 2 only when the R 2 haplotype variant (rs675072G>A) was present. GATA1 motifs were intact in 12 of 13 samples. For one sample with a Del phenotype, a novel RHD c.1-110A>C variant disrupted the GATA1 motif in the promoter which was supported by a lack of a GATA1 supershift in the EMSA and 73% transcriptional activity in the luciferase assay. Two samples were D+/D- chimeras. Conclusion: The bioinformatic predictions enabled the identification of a novel DEL allele, RHD c.1-110A>C, which disrupted the GATA1 motif in the proximal promoter. Although the majority of the samples investigated here remain unexplained, we provide GATA1 targets which may benefit future RHD regulatory investigations.

Epigenetic dissection of human blood group genes reveals regulatory elements and detailed characteristics of KEL and four other loci.

BACKGROUND: Blood typing is essential for safe transfusions and is performed serologically or genetically. Genotyping predominantly focuses on coding regions, but non-coding variants may affect gene regulation, as demonstrated in the ABO, FY and XG systems. To uncover regulatory loci, we expanded a recently developed bioinformatics pipeline for discovery of non-coding variants by including additional epigenetic datasets. METHODS: Multiple datasets including ChIP-seq with erythroid transcription factors (TFs), histone modifications (H3K27ac, H3K4me1), and chromatin accessibility (ATAC-seq) were analyzed. Candidate regulatory regions were investigated for activity (luciferase assays) and TF binding (electrophoretic mobility shift assay, EMSA, and mass spectrometry, MS). RESULTS: In total, 814 potential regulatory sites in 47 blood-group-related genes were identified where one or more erythroid TFs bound. Enhancer candidates in CR1, EMP3, ABCB6, and ABCC4 indicated by ATAC-seq, histone markers, and co-occupancy of 4 TFs (GATA1/KLF1/RUNX1/NFE2) were investigated but only CR1 and ABCC4 showed increased transcription. Co-occupancy of GATA1 and KLF1 was observed in the KEL promoter, previously reported to contain GATA1 and Sp1 sites. TF binding energy scores decreased when three naturally occurring variants were introduced into GATA1 and KLF1 motifs. Two of three GATA1 sites and the KLF1 site were confirmed functionally. EMSA and MS demonstrated increased GATA1 and KLF1 binding to the wild-type compared to variant motifs. DISCUSSION: This combined bioinformatics and experimental approach revealed multiple candidate regulatory regions and predicted TF co-occupancy sites. The KEL promoter was characterized in detail, indicating that two adjacent GATA1 and KLF1 motifs are most crucial for transcription.

Elucidation of the low-expressing erythroid CR1 phenotype by bioinformatic mining of the GATA1-driven blood-group regulome.

Genetic determinants underlying most human blood groups are now clarified but variation in expression levels remains largely unexplored. By developing a bioinformatics pipeline analyzing GATA1/Chromatin immunoprecipitation followed by sequencing (ChIP-seq) datasets, we identify 193 potential regulatory sites in 33 blood-group genes. As proof-of-concept, we aimed to delineate the low-expressing complement receptor 1 (CR1) Helgeson phenotype on erythrocytes, which is correlated with several diseases and protects against severe malaria. We demonstrate that two candidate CR1 enhancer motifs in intron 4 bind GATA1 and drive transcription. Both are functionally abolished by naturally-occurring SNVs. Erythrocyte CR1-mRNA and CR1 levels correlate dose-dependently with genotype of one SNV (rs11117991) in two healthy donor cohorts. Haplotype analysis of rs11117991 with previously proposed markers for Helgeson shows high linkage disequilibrium in Europeans but explains the poor prediction reported for Africans. These data resolve the longstanding debate on the genetic basis of inherited low CR1 and form a systematic starting point to investigate the blood group regulome.

Twisted oxide lateral homostructures with conjunction tunability.

Epitaxial growth is of significant importance over the past decades, given it has been the key process of modern technology for delivering high-quality thin films. For conventional heteroepitaxy, the selection of proper single crystal substrates not only facilitates the integration of different materials but also fulfills interface and strain engineering upon a wide spectrum of functionalities. Nevertheless, the lattice structure, regularity and crystalline orientation are determined once a specific substrate is chosen. Here, we reveal the growth of twisted oxide lateral homostructure with controllable in-plane conjunctions. The twisted lateral homostructures with atomically sharp interfaces can be composed of epitaxial "blocks" with different crystalline orientations, ferroic orders and phases. We further demonstrate that this approach is universal for fabricating various complex systems, in which the unconventional physical properties can be artificially manipulated. Our results establish an efficient pathway towards twisted lateral homostructures, adding additional degrees of freedom to design epitaxial films.

Negatively Charged In-Plane and Out-Of-Plane Domain Walls with Oxygen-Vacancy Agglomerations in a Ca-Doped Bismuth-Ferrite Thin Film.

The interaction of oxygen vacancies and ferroelectric domain walls is of great scientific interest because it leads to different domain-structure behaviors. Here, we use high-resolution scanning transmission electron microscopy to study the ferroelectric domain structure and oxygen-vacancy ordering in a compressively strained Bi0.9Ca0.1FeO3-δ thin film. It was found that atomic plates, in which agglomerated oxygen vacancies are ordered, appear without any periodicity between the plates in out-of-plane and in-plane orientation. The oxygen non-stoichiometry with δ ≈ 1 in FeO2-δ planes is identical in both orientations and shows no preference. Within the plates, the oxygen vacancies form 1D channels in a pseudocubic [010] direction with a high number of vacancies that alternate with oxygen columns with few vacancies. These plates of oxygen vacancies always coincide with charged domain walls in a tail-to-tail configuration. Defects such as ordered oxygen vacancies are thereby known to lead to a pinning effect of the ferroelectric domain walls (causing application-critical aspects, such as fatigue mechanisms and countering of retention failure) and to have a critical influence on the domain-wall conductivity. Thus, intentional oxygen vacancy defect engineering could be useful for the design of multiferroic devices with advanced functionality.

Extremely Fast Optical and Nonvolatile Control of Mixed-Phase Multiferroic BiFeO3 via Instantaneous Strain Perturbation.

Multiferroics-materials that exhibit coupled ferroic orders-are considered to be one of the most promising candidate material systems for next-generation spintronics, memory, low-power nanoelectronics and so on. To advance potential applications, approaches that lead to persistent and extremely fast functional property changes are in demand. Herein, it is revealed that the phase transition and the correlated ferroic orders in multiferroic BiFeO3 (BFO) can be modulated via illumination of single short/ultrashort light pulses. Heat transport simulations and ultrafast optical pump-probe spectroscopy reveal that the transient strain induced by light pulses plays a key role in determining the persistent final states. Having identified the diffusionless phase transformation features via scanning transmission electron microscopy, sequential laser pulse illumination is further demonstrated to perform large-area phase and domain manipulation in a deterministic way. The work contributes to all-optical and rapid nonvolatile control of multiferroicity, offering different routes while designing novel optoelectronics.

A Fast Route Towards Freestanding Single-Crystalline Oxide Thin Films by Using YBa2Cu3O7-x as a Sacrificial Layer.

Researchers have long been seeking multifunctional materials that can be adopted for next-generation nanoelectronics, and which, hopefully, are compatible with current semiconductor processing for further integration. Along this vein, complex oxides have gained numerous attention due to their versatile functionalities. Despite the fact that unbounded potential of complex oxides has been examined over the past years, one of the major challenges lies in the direct integration of these functional oxides onto existing devices or targeted substrates that are inherently incompatible in terms of oxide growth. To fulfill this goal, freestanding processes have been proposed, in which wet etching of inserted sacrificial layers is regarded as one of the most efficient ways to obtain epitaxial high-quality thin films. In this study, we propose using an alternative oxide, YBa2Cu3O7 (YCBO), as a sacrificial layer, which can be easily dissolved in light hydrochloric acid in a more efficient way, while protecting selected complex oxides intact. The high epitaxial quality of the selected complex oxide before and after freestanding process using YBCO as a sacrificial layer is comprehensively studied via a combination of atomic force microscopy, X-ray diffraction, transmission electron microscopy, and electrical transports. This approach enables direct integration of complex oxides with arbitrary substrates and devices and is expected to offer a faster route towards the development of low-dimensional quantum materials.

Genotyping and serotyping profiles showed weak Jka presentation for previously typed as Jknull donors.

BACKGROUND AND OBJECTIVES: Kidd blood group system consists of two major antigens: Jka and Jkb . Both the antigens are absent in individuals typed as Jknull and may develop clinically significant anti-Jk3 antibody. Screening donors for provision of Jknull blood is an ongoing task for blood centres with Jknull blood units kept frozen for specific requirements. In 2016, we discovered a previously typed Jknull donor to be Jka weak positive. Therefore, a study was conducted for our donors to verify Jknull status and to reinforce our typing protocol. MATERIALS AND METHODS: In this experiment, donors previously typed and screened as Jknull were tested with four antisera of Jka and Jkb , and each with gel card for serology testing. Sequence analysis was performed for SLC14A1 gene for the detection of JKnull and weak alleles for genetic testing. RESULTS: Among the 30 samples, four were serologically identified as Jk(a+w ) and genotypically identified as heterozygous for the JK*01W.01 allele. The other 26 were confirmed to be Jknull with JK*02N.01 as the most frequent allele. None of JK*B weak alleles were detected, but three were identified as false positives in the tube method. Gel card gave great accuracy for Jkb detection, but failed to give consistent results for weak Jka . CONCLUSION: By combining the tube method and gel card method in serology, along with complementary genetic testing, the possibility of misinterpreting weak Jka expression was eliminated, and we were able to provide Jknull blood for safe clinical transfusion.

HAHap: a read-based haplotyping method using hierarchical assembly.

BACKGROUND: The need for read-based phasing arises with advances in sequencing technologies. The minimum error correction (MEC) approach is the primary trend to resolve haplotypes by reducing conflicts in a single nucleotide polymorphism-fragment matrix. However, it is frequently observed that the solution with the optimal MEC might not be the real haplotypes, due to the fact that MEC methods consider all positions together and sometimes the conflicts in noisy regions might mislead the selection of corrections. To tackle this problem, we present a hierarchical assembly-based method designed to progressively resolve local conflicts. RESULTS: This study presents HAHap, a new phasing algorithm based on hierarchical assembly. HAHap leverages high-confident variant pairs to build haplotypes progressively. The phasing results by HAHap on both real and simulated data, compared to other MEC-based methods, revealed better phasing error rates for constructing haplotypes using short reads from whole-genome sequencing. We compared the number of error corrections (ECs) on real data with other methods, and it reveals the ability of HAHap to predict haplotypes with a lower number of ECs. We also used simulated data to investigate the behavior of HAHap under different sequencing conditions, highlighting the applicability of HAHap in certain situations.

Transparent Antiradiative Ferroelectric Heterostructure Based on Flexible Oxide Heteroepitaxy.

In the era of Internet of Things, the demand for flexible and transparent electronic devices has shifted to the forefront of materials science research. However, the radiation damage to key performance of transparent devices under radiative environment remains as a critical issue. Here, we present a promising technology for nonvolatile transparent electronic devices based on flexible oxide heteroepitaxy. A direct fabrication of epitaxial lead lanthanum zirconate titanate on transparent flexible mica substrate with indium tin oxide electrodes is presented. The transparent flexible ferroelectric heterostructures not only retain their superior performance, thermal stability, reliability, and mechanical durability, but also exhibit remarkably robust properties against to a strong radiation exposure. Our study demonstrates an extraordinary concept to realize transparent flexible nonvolatile electronic devices for the design and development of next-generation smart devices with potential application in electronics, automotive, aerospace, and nuclear systems.

ABO genotyping with next-generation sequencing to resolve heterogeneity in donors with serology discrepancies.

BACKGROUND: ABO subtypes are characterized by the alteration of antigens present and their expression levels on red blood cells and many are linked to genetic changes in the ABO gene. Weakened expression of antigens should be identified to prevent transfusion reactions or ABO-incompatible transplantations. Genotyping can be applied to identify subtypes to complement serologic testing. Next-generation sequencing (NGS) has shown to provide sensitive and accurate genotyping results as well as valuable cis/trans information. Here we took advantage of NGS and applied it to resolve serology discrepancies in ABO typing. STUDY DESIGN AND METHODS: In this study, we customized capture probes targeting the entire ABO gene and sequenced on MiSeq Illumina. The subtype-causing variants were identified, and cis/trans association to ABO alleles was determined. The results from NGS, serology, and Sanger sequencing were compared. RESULTS: Four control samples typed A, B, O, and AB were correctly genotyped. Of 24 serologically discrepant samples, subtype-causing variations were found in 20 cases, with two unresolved and two identified as weakening of ABO antibody in reverse. The types of variations include 17 known subtype alleles, one novel variant, one novel large deletion, and one microchimerism. Haplotypes encompassing Exons 6 and 7 of ABO were reconstructed in 17 of the 20 samples. CONCLUSION: This study demonstrated a full coverage of ABO by capture-based panel, phasing analysis with NGS in ABO genotyping resolved heterogeneity with novel allele and microchimerism findings. This approach provided a more precise method for subtyping and thereby leading to safer transfusion.

Heteroepitaxy of Fe3O4/Muscovite: A New Perspective for Flexible Spintronics.

Spintronics has captured a lot of attention since it was proposed. It has been triggering numerous research groups to make their efforts on pursuing spin-related electronic devices. Recently, flexible and wearable devices are in a high demand due to their outstanding potential in practical applications. In order to introduce spintronics into the realm of flexible devices, we demonstrate that it is feasible to grow epitaxial Fe3O4 film, a promising candidate for realizing spintronic devices based on tunneling magnetoresistance, on flexible muscovite. In this study, the heteroepitaxy of Fe3O4/muscovite is characterized by X-ray diffraction, high-resolution transmission electron microscopy, and Raman spectroscopy. The chemical composition and magnetic feature are investigated by a combination of X-ray photoelectron spectroscopy and X-ray magnetic circular dichroism. The electrical and magnetic properties are examined to show the preservation of the primitive properties of Fe3O4. Furthermore, various bending tests are performed to show the tunability of functionalities and to confirm that the heterostructures retain the physical properties under repeated cycles. These results illustrate that the Fe3O4/muscovite heterostructure can be a potential candidate for the applications in flexible spintronics.

Magnetic mesocrystal-assisted magnetoresistance in manganite.

Mesocrystal, a new class of crystals as compared to conventional and well-known single crystals and polycrystalline systems, has captured significant attention in the past decade. Recent studies have been focused on the advance of synthesis mechanisms as well as the potential on device applications. In order to create further opportunities upon functional mesocrystals, we fabricated a self-assembled nanocomposite composed of magnetic CoFe2O4 mesocrystal in Sr-doped manganites. This combination exhibits intriguing structural and magnetic tunabilities. Furthermore, the antiferromagnetic coupling of the mesocrystal and matrix has induced an additional magnetic perturbation to spin-polarized electrons, resulting in a significantly enhanced magnetoresistance in the nanocomposite. Our work demonstrates a new thought toward the enhancement of intrinsic functionalities assisted by mesocrystals and advanced design of novel mesocrystal-embedded nanocomposites.

Measurement of organic chemical refractive indexes using an optical time-domain reflectometer.

In this investigation, we propose and experimentally demonstrate a method for measuring the refractive index (RI) of liquid organic chemicals. The scheme is based on a single-mode fiber (SMF) sensor and an optical time-domain reflectometer (OTDR). Here, due to the different reflectance (R) between the SMF and organic liquid chemicals, the reflected power level of the backscattering light (BSL) measured by the OTDR would be different. Therefore, we can measure the RI of chemical under test via the measured BSL level. The proposed RI sensor is simple and easy to manipulate, with stable detected signals, and has the potential to be a valuable tool for use in biological and chemical applications.

A simple fiber Bragg grating-based sensor network architecture with self-protecting and monitoring functions.

A novel fiber Bragg grating (FBG)-based passive sensor architecture, which can be used to protect the fiber cut and monitor the multiple sensors simultaneously, is proposed and experimentally demonstrated. Here, we employ a wavelength-tunable erbium-doped fiber (EDF) laser scheme with 25 km cavity length acting as the detecting light source in central office (CO). Each FBG sensor, serving as a feedback element, is used in proposed sensor architecture. By tuning the tunable bandpass filter (TBF) placing inside cavity to match the corresponding Bragg wavelength of FBG over the amplification bandwidth, we can retrieve the related wavelength lasing for the FBG sensing and monitoring simultaneously. Moreover, the survivability and capacity of the passive FBG sensor architecture can be also enhanced.