Resonant Raman scattering of few layers CrBr3.

We investigate the vibrational and magnetic properties of thin layers of chromium tribromide (CrBr3) with a thickness ranging from three to twenty layers (3-20 L) revealed by the Raman scattering (RS) technique. Systematic dependence of the RS process efficiency on the energy of the laser excitation is explored for four different excitation energies: 1.96 eV, 2.21 eV, 2.41 eV, and 3.06 eV. Our characterization demonstrates that for 12 L CrBr3, 3.06 eV excitation could be considered resonant with interband electronic transitions due to the enhanced intensity of the Raman-active scattering resonances and the qualitative change in the Raman spectra. Polarization-resolved RS measurements for 12 L CrBr3 and first-principles calculations allow us to identify five observable phonon modes characterized by distinct symmetries, classified as the A g and E g modes. The evolution of phonon modes with temperature for a 16 L CrBr3 encapsulated in hexagonal boron nitride flakes demonstrates alterations of phonon energies and/or linewidths of resonances indicative of a transition between the paramagnetic and ferromagnetic state at Curie temperature ( T C ≈ 50  K). The exploration of the effects of thickness on the phonon energies demonstrated small variations pronounces exclusively for the thinnest layers in the vicinity of 3-5 L. We propose that this observation can be due to the strong localization in the real space of interband electronic excitations, limiting the effects of confinement for resonantly excited Raman modes to atomically thin layers.

CRISPR/Cas9 screen for genome-wide interrogation of essential MYC-bound E-boxes in cancer cells.

The transcription factor MYC is a proto-oncogene with a well-documented essential role in the pathogenesis and maintenance of several types of cancer. MYC binds to specific E-box sequences in the genome to regulate gene expression in a cell-type- and developmental-stage-specific manner. To date, a combined analysis of essential MYC-bound E-boxes and their downstream target genes important for growth of different types of cancer is missing. In this study, we designed a CRISPR/Cas9 library to destroy E-box sequences in a genome-wide fashion. In parallel, we used the Brunello library to knock out protein-coding genes. We performed high-throughput screens with these libraries in four MYC-dependent cancer cell lines-K562, ST486, HepG2, and MCF7-which revealed several essential E-boxes and genes. Among them, we pinpointed crucial common and cell-type-specific MYC-regulated genes involved in pathways associated with cancer development. Extensive validation of our approach confirmed that E-box disruption affects MYC binding, target-gene expression, and cell proliferation in vitro as well as tumor growth in vivo. Our unique, well-validated tool opens new possibilities to gain novel insights into MYC-dependent vulnerabilities in cancer cells.

TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs.

Eukaryotic genomes contain several types of recurrent sequence motifs, e.g. transcription factor motifs, miRNA binding sites, repetitive elements. CRISPR/Cas9 can facilitate identification and study of crucial motifs. We present transCRISPR, the first online tool dedicated to search for sequence motifs in the user-provided genomic regions and design optimal sgRNAs targeting them. Users can obtain sgRNAs for chosen motifs, for up to tens of thousands of target regions in 30 genomes, either for the Cas9 or dCas9 system. TransCRISPR provides user-friendly tables and visualizations, summarizing features of identified motifs and designed sgRNAs such as genomic localization, quality scores, closest transcription start sites and others. Experimental validation of sgRNAs for MYC binding sites designed with transCRISPR confirmed efficient disruption of the targeted motifs and effect on expression of MYC-regulated genes. TransCRISPR is available from https://transcrispr.igcz.poznan.pl/transcrispr/.

In vivo secondary structural analysis of Influenza A virus genomic RNA.

Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA-targeting antivirals. Chemical RNA mapping using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) coupled with Mutational Profiling (MaP) allows for the thorough examination of secondary structures in low-abundance RNAs in their biological context. So far, the method has been used for analyzing the RNA secondary structures of several viruses including SARS-CoV-2 in virio and in cellulo. Here, we used SHAPE-MaP and dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) for genome-wide secondary structure analysis of viral RNA (vRNA) of the pandemic influenza A/California/04/2009 (H1N1) strain in both in virio and in cellulo environments. Experimental data allowed the prediction of the secondary structures of all eight vRNA segments in virio and, for the first time, the structures of vRNA5, 7, and 8 in cellulo. We conducted a comprehensive structural analysis of the proposed vRNA structures to reveal the motifs predicted with the highest accuracy. We also performed a base-pairs conservation analysis of the predicted vRNA structures and revealed many highly conserved vRNA motifs among the IAVs. The structural motifs presented herein are potential candidates for new IAV antiviral strategies.

The effect of temperature and excitation energy on Raman scattering in bulkHfS2.

Raman scattering (RS) in bulk hafnium disulfide (HfS2) is investigated as a function of temperature (5 K - 350 K) with polarization resolution and excitation of several laser energies. An unexpected temperature dependence of the energies of the main Raman-active (A1gand Eg) modes with the temperature-induced blueshift in the low-temperature limit is observed. The low-temperature quenching of a modeω1(134 cm-1) and the emergence of a new mode at approx. 184 cm-1, labeledZ, is reported. The optical anisotropy of the RS inHfS2is also reported, which is highly susceptible to the excitation energy. The apparent quenching of the A1gmode atT = 5 K and of the Egmode atT= 300 K in the RS spectrum excited with 3.06 eV excitation is also observed. We discuss the results in the context of possible resonant character of light-phonon interactions. Analyzed is also a possible effect of the iodine molecules intercalated in the van der Waals gaps between neighboringHfS2layers, which inevitably result from the growth procedure.

Electronic and Excitonic Properties of MSi2 Z4 Monolayers.

MA2 Z4 monolayers form a new class of hexagonal non-centrosymmetric materials hosting extraordinary spin-valley physics. While only two compounds (MoSi2 N4 and WSi2 N4 ) are recently synthesized, theory predicts interesting (opto)electronic properties of a whole new family of such two-dimensional (2D) materials. Here, the chemical trends of band gaps and spin-orbit splittings of bands in selected MSi2 Z4 (M = Mo, W; Z = N, P, As, Sb) compounds are studied from first-principles. Effective Bethe-Salpeter-equation-based calculations reveal high exciton binding energies. Evolution of excitonic energies under external magnetic field is predicted by providing their effective g-factors and diamagnetic coefficients, which can be directly compared to experimental values. In particular, large positive g-factors are predicted for excitons involving higher conduction bands. In view of these predictions, MSi2 Z4 monolayers yield a new platform to study excitons and are attractive for optoelectronic devices, also in the form of heterostructures. In addition, a spin-orbit induced bands inversion is observed in the heaviest studied compound, WSi2 Sb4 , a hallmark of its topological nature.

Stress-Tuned Optical Transitions in Layered 1T-MX2 (M=Hf, Zr, Sn; X=S, Se) Crystals.

Optical measurements under externally applied stresses allow us to study the materials' electronic structure by comparing the pressure evolution of optical peaks obtained from experiments and theoretical calculations. We examine the stress-induced changes in electronic structure for the thermodynamically stable 1T polytype of selected MX2 compounds (M=Hf, Zr, Sn; X=S, Se), using the density functional theory. We demonstrate that considered 1T-MX2 materials are semiconducting with indirect character of the band gap, irrespective to the employed pressure as predicted using modified Becke-Johnson potential. We determine energies of direct interband transitions between bands extrema and in band-nesting regions close to Fermi level. Generally, the studied transitions are optically active, exhibiting in-plane polarization of light. Finally, we quantify their energy trends under external hydrostatic, uniaxial, and biaxial stresses by determining the linear pressure coefficients. Generally, negative pressure coefficients are obtained implying the narrowing of the band gap. The semiconducting-to-metal transition are predicted under hydrostatic pressure. We discuss these trends in terms of orbital composition of involved electronic bands. In addition, we demonstrate that the measured pressure coefficients of HfS2 and HfSe2 absorption edges are in perfect agreement with our predictions. Comprehensive and easy-to-interpret tables containing the optical features are provided to form the basis for assignation of optical peaks in future measurements.

Strain-Induced Exciton Hybridization in WS_{2} Monolayers Unveiled by Zeeman-Splitting Measurements.

Mechanical deformations and ensuing strain are routinely exploited to tune the band gap energy and to enhance the functionalities of two-dimensional crystals. In this Letter, we show that strain leads also to a strong modification of the exciton magnetic moment in WS_{2} monolayers. Zeeman-splitting measurements under magnetic fields up to 28.5 T were performed on single, one-layer-thick WS_{2} microbubbles. The strain of the bubbles causes a hybridization of k-space direct and indirect excitons resulting in a sizable decrease in the modulus of the g factor of the ground-state exciton. These findings indicate that strain may have major effects on the way the valley number of excitons can be used to process binary information in two-dimensional crystals.

Temperature induced modulation of resonant Raman scattering in bilayer 2H-MoS2.

The temperature evolution of the resonant Raman scattering from high-quality bilayer 2H-MoS[Formula: see text] encapsulated in hexagonal BN flakes is presented. The observed resonant Raman scattering spectrum as initiated by the laser energy of 1.96 eV, close to the A excitonic resonance, shows rich and distinct vibrational features that are otherwise not observed in non-resonant scattering. The appearance of 1st and 2nd order phonon modes is unambiguously observed in a broad range of temperatures from 5 to 320 K. The spectrum includes the Raman-active modes, i.e. E[Formula: see text]([Formula: see text]) and A[Formula: see text]([Formula: see text]) along with their Davydov-split counterparts, i.e. E[Formula: see text]([Formula: see text]) and B[Formula: see text]([Formula: see text]). The temperature evolution of the Raman scattering spectrum brings forward key observations, as the integrated intensity profiles of different phonon modes show diverse trends. The Raman-active A[Formula: see text]([Formula: see text]) mode, which dominates the Raman scattering spectrum at T = 5 K quenches with increasing temperature. Surprisingly, at room temperature the B[Formula: see text]([Formula: see text]) mode, which is infrared-active in the bilayer, is substantially stronger than its nominally Raman-active A[Formula: see text]([Formula: see text]) counterpart.

SINBAD, structural, experimental and clinical characterization of STAT inhibitors and their potential applications.

The abnormal activation of signal transducer and activator of transcription (STAT) protein family is recognized as cause or driving force behind multiple diseases progression. Therefore, searching for potential treatment strategy is pursued by multiple scientific groups. We consider that providing comprehensive, integrated and unified dataset for STAT inhibitory compounds may serve as important tool for other researchers. We developed SINBAD (STAT INhbitor Biology And Drug-ability) in response to our experience with inhibitory compound research, knowing that gathering detailed information is crucial for effective experiment design and also for finding potential solutions in case of obtaining inconclusive results. SINBAD is a curated database of STAT inhibitors which have been published and described in scientific articles providing prove of their inhibitory properties. It is a tool allowing easy analysis of experimental conditions and provides detailed information about known STAT inhibitory compounds.

Strong Substrate Strain Effects in Multilayered WS2 Revealed by High-Pressure Optical Measurements.

The optical properties of two-dimensional materials can be effectively tuned by strain induced from a deformable substrate. In the present work we combine first-principles calculations based on density functional theory and the effective Bethe-Salpeter equation with high-pressure optical measurements to thoroughly describe the effect of strain and dielectric environment onto the electronic band structure and optical properties of a few-layered transition-metal dichalcogenide. Our results show that WS2 remains fully adhered to the substrate at least up to a -0.6% in-plane compressive strain for a wide range of substrate materials. We provide a useful model to describe effect of strain on the optical gap energy. The corresponding experimentally determined out-of-plane and in-plane stress gauge factors for WS2 monolayers are -8 and 24 meV/GPa, respectively. The exceptionally large in-plane gauge factor confirms transition metal dichalcogenides as very promising candidates for flexible functionalities. Finally, we discuss the pressure evolution of an optical transition closely lying to the A exciton for bulk WS2 as well as the direct-to-indirect transition of the monolayer upon compression.

Human live spermatozoa morphology assessment using digital holographic microscopy.

Digital holographic microscopy (DHM) was applied for the morphological assessment of live intact spermatozoa from fertile and infertile men directly after semen liquefaction. This method allowed us to study the sperm population directly from the sample droplet and not only from the focal plane of the microscope as in classical optical microscopy. The newly implemented 3-dimensional sperm morphological parameters (head height, acrosome/nucleus height, head/midpiece height) were included in morphological assessment of semen samples from fertile and infertile individuals. The values of the 3D parameters were less variable in fertile men than for infertile ones. DHM was also used to compare the morphological profiles of spermatozoa after applying the "swim-up" and gradient centrifugation techniques. During selection, the most statistically significant differences were observed after separation with a Percoll gradient of 90% and a 60-min "swim-up" procedure versus 'native' unfractionated samples. This shows that the developed methodology can be efficiently used for the selection of morphologically sound spermatozoa. The motility type for each spermatozoon was also assessed. The results indicate that the extension of the number of morphological parameters with new 3D parameters and the simultaneous assessment of sperm motility may be valuable addition to sperm examination.

A new molecular mechanism of RNA circularization and the microRNA sponge formation.

A new mechanism of RNA circularization driven by specific binding of miRNAs is described. We identified the 71 CUUCC pentanucleotide motifs distributed regularly throughout the entire molecule of CDR1as RNA that bind to 71 miRNAs through their seed sequence GGAAG. The sequential binding of miR-7 RNAs (71 molecules) brings both ends of CDR1as RNA (1 molecule) together and stimulate phosphodiester bond formation between nucleotides C1 and A1299 at the 5' and 3' end, respectively. The binding of miRNAs to CDR1as RNA results in the unique complex formation, which shows three specific structural domains: (i) two short helixes with an internal loop, (ii) the hinge, and (iii) the triple-helix. The proposed mechanism explains specific RNA circularization and its function as a miRNAs sponge. Furthermore, the existing wet experimental data on the interaction of CDR1as RNA with miR-7 fully supports our observation. Although miR-671 shows the same seed sequence as miR-7, it forms an almost perfect double helix with CDR1as RNA and induces the cleavage of CDR1as, but does not stimulate circularization. To check how common is the proposed mechanism among circular RNAs, we analyzed the most recent circAtlas database counting almost 1.1 million sequences. It turned out that there are a huge number of circRNAs, which showed miRNAs seed binding sequences distributed through the whole circRNA sequences and prove that circularization of linear transcript is miRNA dependent.Communicated by Ramaswamy H. Sarma.

Anisotropic Optical and Vibrational Properties of GeS.

The optical response of bulk germanium sulfide (GeS) is investigated systematically using different polarization-resolved experimental techniques, such as photoluminescence (PL), reflectance contrast (RC), and Raman scattering (RS). It is shown that while the low-temperature (T = 5 K) optical band-gap absorption is governed by a single resonance related to the neutral exciton, the corresponding emission is dominated by the disorder/impurity- and/or phonon-assisted recombination processes. Both the RC and PL spectra are found to be linearly polarized along the armchair direction. The measured RS spectra over a broad range from 5 to 300 K consist of six Raman peaks identified with the help of Density Functional Theory (DFT) calculations: Ag1, Ag2, Ag3, Ag4, B1g1, and B1g2, which polarization properties are studied under four different excitation energies. We found that the polarization orientations of the Ag2 and Ag4 modes under specific excitation energy can be useful tools to determine the GeS crystallographic directions: armchair and zigzag.

RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix.

BACKGROUND: The functions of RNA molecules are mainly determined by their secondary structures. These functions can also be predicted using bioinformatic tools that enable the alignment of multiple RNAs to determine functional domains and/or classify RNA molecules into RNA families. However, the existing multiple RNA alignment tools, which use structural information, are slow in aligning long molecules and/or a large number of molecules. Therefore, a more rapid tool for multiple RNA alignment may improve the classification of known RNAs and help to reveal the functions of newly discovered RNAs. RESULTS: Here, we introduce an extremely fast Python-based tool called RNAlign2D. It converts RNA sequences to pseudo-amino acid sequences, which incorporate structural information, and uses a customizable scoring matrix to align these RNA molecules via the multiple protein sequence alignment tool MUSCLE. CONCLUSIONS: RNAlign2D produces accurate RNA alignments in a very short time. The pseudo-amino acid substitution matrix approach utilized in RNAlign2D is applicable for virtually all protein aligners.

Experimental and Theoretical Studies of the Electronic Band Structure of Bulk and Atomically Thin Mo1-x W x Se2 Alloys.

We present studies focused on the evolution of the electronic band structure of the Mo1-x W x Se2 alloy with the tungsten content, which was conducted by combining experimental and theoretical methods. Employed spectroscopic techniques, namely, photoreflectance, photoacoustic spectroscopy, and photoluminescence, allowed observing indirect and direct transitions at high and beyond high-symmetry points of the Brillouin zone (BZ). Two excitons (A and B) associated with the K point of the BZ were observed together with other optical transitions (C and D) related to band nesting. Moreover, we have also identified the indirect transition for the studied crystals. Obtained energies for all transitions were tracked with a tungsten content and compared with results of calculations performed within density functional theory. Furthermore, based on the mentioned comparison, optical transitions were assigned to specific regions of the BZ. Finally, we have obtained bowing parameters for experimentally observed features, for, i.e., thin-film samples: b(A) = 0.13 ± 0.03 eV, b(B) = 0.14 ± 0.03 eV, b(C) = 0.044 ± 0.008 eV, and b(D) = 0.010 ± 0.003 eV.

Excitonic Complexes in n-Doped WS2 Monolayer.

We investigate the origin of emission lines apparent in the low-temperature photoluminescence spectra of n-doped WS2 monolayer embedded in hexagonal BN layers using external magnetic fields and first-principles calculations. Apart from the neutral A exciton line, all observed emission lines are related to the negatively charged excitons. Consequently, we identify emissions due to both the bright (singlet and triplet) and dark (spin- and momentum-forbidden) negative trions as well as the phonon replicas of the latter optically inactive complexes. The semidark trions and negative biexcitons are distinguished. On the basis of their experimentally extracted and theoretically calculated g-factors, we identify three distinct families of emissions due to exciton complexes in WS2: bright, intravalley, and intervalley dark. The g-factors of the spin-split subbands in both the conduction and valence bands are also determined.

Beta-defensin 1 gene polymorphisms in the pathologies of the oral cavity-Data from meta-analysis: Association only with rs1047031 not with rs1800972, rs1799946, and rs11362.

OBJECTIVES: The purpose of this meta-analysis was to reveal a potential association of the four functional polymorphisms in human Beta-defensin 1 (DEFB1) gene: rs1047031(c*5G > A) at 3'UTR and rs11362 (-20 G > A), rs1800972(-44 C > G), and rs1799946 (-52 G > A) at 5'UTR with the risk of common oral cavity pathologies that included periodontitis, caries, lichen planus, and recurrent aphthous stomatitis. METHODS: The relevant studies were obtained by the two researchers from PubMed, Scopus, and Web of Science up to April 29, 2020. The manual search of the reference lists was also performed. Studies on DEFB1 gene polymorphisms and oral cavity disorders, using the case-control genetic association analysis approach, and published as full texts in English were included. To assess the association strength, odds ratios (ORs) with their 95% confidence intervals (CIs) were extracted. RESULTS: Thirteen publications met the inclusion criteria and were incorporated in this meta-analysis. Statistically significant values of the association tests were found only for the rs1047031 polymorphism. Allele distribution in the rs1047031 polymorphism was significantly associated with susceptibility to oral cavity pathologies (adjusted P value = 0.003). The rare variant allele carriers had a significantly higher risk for oral disasters under recessive (CC vs CT + TT), and CC vs CT models. No significant correlations between rs11362, rs1800972, and rs1799946 and the risk of oral pathologies were revealed. CONCLUSIONS: Significant association between rs1047031 polymorphism and risk of oral pathologies has been found, and therefore, we suggest to include this polymorphism in future research concerning the genetic background of the oral cavity diseases.

Seminal Plasma Analysis of Oxidative Stress in Different Genitourinary Topographical Regions Involved in Reproductive Tract Disorders Associated with Genital Heat Stress.

The pathophysiological mechanisms responsible for male subfertility/infertility caused by or complicated by genital heat stress remains unclear in many respects. Because seminal plasma creates the environment for the proper functioning of spermatozoa, in this study, we verified the associations among standard spermiograms, seminal biochemical parameters (neutral alpha-glucosidase, fructose, and citric acid) and oxidative stress markers (total antioxidant capacity, catalase activity, superoxide dismutase activity, and malondialdehyde concentration) in distinct entities associated with male infertility with and without long-time exposure to local hyperthermia. We demonstrated that men exposed to prolonged environmental or clinically recognized local heat stress in adulthood may suffer from dysregulation of seminal antioxidant components, which can be directly associated with epididymal and prostate function. The comparative analysis of the studied parameters showed numerous correlations among all biochemical parameters (particularly neutral alpha-glucosidase) with low standard semen quality in almost all the investigated infertile groups. In light of the data obtained in this originally designed study, we conclude that more attention should be paid to the epididymis and accessory gland function in subfertile and infertile men exposed to genital heat stress, especially in the context of novel treatment algorithms (targeted therapies).