Half Of Sites Research Articles

Recruitment of homodimeric proneural factors by conserved CAT-CAT E-boxes drives major epigenetic reconfiguration in cortical neurogenesis.

Proneural factors of the basic helix-loop-helix family coordinate neurogenesis and neurodifferentiation. Among them, NEUROG2 and NEUROD2 subsequently act to specify neurons of the glutamatergic lineage. Disruption of these factors, their target genes and binding DNA motifs has been linked to various neuropsychiatric disorders. Proneural factors bind to specific DNA motifs called E-boxes (hexanucleotides of the form CANNTG, composed of two CAN half sites on opposed strands). While corticogenesis heavily relies on E-box activity, the collaboration of proneural factors on different E-box types and their chromatin remodeling mechanisms remain largely unknown. Here, we conducted a comprehensive analysis using chromatin immunoprecipitation followed bysequencing (ChIP-seq) data for NEUROG2 and NEUROD2, along with time-matched single-cell RNA-seq, ATAC-seq and DNA methylation data from the developing mouse cortex. Our findings show that these factors are highly enriched in transiently active genomic regions during intermediate stages of neuronal differentiation. Although they primarily bind CAG-containing E-boxes, their binding in dynamic regions is notably enriched in CAT-CAT E-boxes (i.e. CATATG, denoted as 5'3' half sites for dimers), which undergo significant DNA demethylation and exhibit the highest levels of evolutionary constraint. Aided by HT-SELEX data reanalysis, structural modeling and DNA footprinting, we propose that these proneural factors exert maximal chromatin remodeling influence during intermediate stages of neurogenesis by binding as homodimers to CAT-CAT motifs. This study provides an in-depth integrative analysis of the dynamic regulation of E-boxes during neuronal development, enhancing our understanding of the mechanisms underlying the binding specificity of critical proneural factors.

Association of Peri-Implant Mucosa Dimensions With Emergence Profile Angles of the Implant Prosthesis.

The primary aim of this cross-sectional study was to investigate the association between prosthesis design and peri-implant mucosa dimensions and morphology. The secondary aim was to investigate associations between mucosal dimensions and the presence of mucositis. Forty-seven patients with 103 posterior bone level implants underwent clinical and radiographic examination, including cone beam computer tomography and intraoral optical scanning. Three-dimensional models for each implant and peri-implant mucosa were constructed. Vertical mucosa height (TH), horizontal mucosa width at implant platform (TW), and 1.5 mm coronal of the platform (TW1.5), as well as mucosal emergence angle (MEA),deep angle (DA), and total contour angle (TA) were measured at six sites for each implant. There was a consistent correlation between peri-implant mucosa width and height (β = 0.217, p < 0.001), with the width consistently surpassing height by a factor of 1.4-2.1. All three angles (MEA, DA, TA) were negatively associated with mucosa height (p < 0.001), while DA was negatively associated with mucosa width (TW1.5) (p < 0.001, β = -0.02, 95% CI: -0.03, -0.01). There was a significant negative association between bleeding on probing (BoP) and mucosa width at platform (OR 0.903, 95% CI: 0.818-0.997, p = 0.043) and 1.5 coronal (OR 0.877,95% CI: 0.778-0.989, p = 0.033). Implants with less than half sites positive for BoP (0-2/6) had significantly higher mucosa height (OR 3.51, 95% CI: 1.72-7.14,p = 0.001). Prosthesis design can influence the dimensions of the peri-implant mucosa, with wider emergence profile angles associated with reduced peri-implant mucosa height. In particular, a wider deep angle is associated with reduced mucosa width in posterior sites. Reduced peri-implant mucosa height and width are associated with more signs of inflammation. Registered in Thai Clinical Trials Registry: http://www.thaiclinicaltrials.org/show/TCTR20220204002.

Activity of the pleiotropic drug resistance transcription factors Pdr1p and Pdr3p is modulated by binding site flanking sequences.

The transcription factors Pdr1p and Pdr3p regulate pleiotropic drug resistance (PDR) in Saccharomyces cerevisiae via the PDR responsive elements (PDREs) to modulate gene expression. However, the exact mechanisms underlying the differences in their regulons remain unclear. Employing genomic occupancy profiling (CUT&RUN), binding assays, and transcription studies, we characterized the differences in sequence specificity between transcription factors. Findings reveal distinct preferences for core PDRE sequences and the flanking sequences for both proteins. While flanking sequences moderately alter DNA binding affinity, they significantly impact Pdr1/3p transcriptional activity. Notably, both proteins demonstrated the ability to bind half sites, showing potential enhancement of transcription from adjacent PDREs. This insight sheds light on ways Pdr1/3p can differentially regulate PDR.

FIELD AND MODEL RESEARCH OF THE GROUNDWATER FLOWS IN THE AREA OF THE PAKS-2 NPP CONSTRUCTION, HUNGARY

The construction of the nuclear power plant (NPP) requires conducting a large number of engineering and hydrogeological surveys, as well as assessment of the design decisions’ safety. A deep excavation pit at the Paks II NPP construction site requires execution of the cut-off wall due to extremely high groundwater saturation of the alluvial deposits. However, lithological anisotropy and the presence of dislocation zones did not allow identifying the appropriate depth for the cut-off wall construction. Unfortunately, engineering geological boreholes with a 20-meter distance between them and surface and borehole geophysical surveys could not identify the hydrogeological units. Thus, to conceptualize the hydrogeological settings, an analysis of the groundwater head distribution and the large-scale pumping tests were conducted. The interpretation of the geological data and the distinguishing of the hydrogeological units were carried out iteratively using the hydrogeological numerical model. The flow model could represent the hydraulic head distribution, the response of the lithologically heterogeneous layers to the water fluctuations in the Danube river, and the pumping tests carried out at the different depths. The results of the hydrogeological modeling revealed the aquitard to be continuous throughout the territory; however, its top’s depth changes from 30–35 to 90 m within the construction site of the Paks II NPP. This complex geometry of the aquitard is controlled by the plicated dislocation zone, which cuts the construction site in half and is revealed as the right wall of the graben.Correct hydrogeological stratification enabled us to ensure waterproof activities such as the cut-off wall construction using the hydrogeological model when excavating a deep pit for the Paks II NPP. This also minimizes the hydrodynamic impact on the closely located NPP Paks in operation.

SARS-CoV-2 papain-like protease plays multiple roles in regulating cellular proteins in the endoplasmic reticulum

Nsp3s are the largest nonstructural proteins of coronaviruses. These transmembrane proteins include papain-like proteases (PLpro) that play essential roles in cleaving viral polyproteins into their mature units. The PLpro of SARS-CoV viruses also have deubiquitinating and deISGylating activities. As Nsp3 is an endoplasmic reticulum (ER)-localized protein, we asked if the deubiquitinating activity of SARS-CoV-2 PLpro affects proteins that are substrates for ER-associated degradation (ERAD). Using full-length Nsp3 as well as a truncated transmembrane form we interrogated, by coexpression, three potential ERAD substrates, all of which play roles in regulating lipid biosynthesis. Transmembrane PLpro increases the level of INSIG-1 and decreases its ubiquitination. However, different effects were seen with SREBP-1 and SREBP-2. Transmembrane PLpro cleaves SREBP-1 at three sites, including two noncanonical sites in the N-terminal half of the protein, resulting in a decrease in precursors of the active transcription factor. Conversely, cleavage of SREBP-2 occurs at a single canonical site that disrupts a C-terminal degron, resulting in increased SREBP-2 levels. When this site is mutated and the degron can no longer be interrupted, SREBP-2 is still stabilized by transmembrane PLpro, which correlates with a decrease in SREBP-2 ubiquitination. All of these observations are dependent on PLpro catalytic activity. Our findings demonstrate that, when anchored to the ER membrane, SARS-CoV-2 Nsp3 PLpro can function as a deubiquitinating enzyme to stabilize ERAD substrates. Additionally, SARS-CoV-2 Nsp3 PLpro can cleave ER-resident proteins, including at sites that could escape analyses based on the established consensus sequence.

Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode.

Gene expression changes are orchestrated by transcription factors (TFs), which bind to DNA to regulate gene expression. It remains surprisingly difficult to predict basic features of the transcriptional process, including in vivo TF occupancy. Existing thermodynamic models of TF function are often not concordant with experimental measurements, suggesting undiscovered biology. Here, we analyzed one of the most well-studied TFs, the yeast zinc cluster Gal4, constructed a Shea-Ackers thermodynamic model to describe its binding, and compared the results of this model to experimentally measured Gal4p binding in vivo. We found that at many promoters, the model predicted no Gal4p binding, yet substantial binding was observed. These outlier promoters lacked canonical binding motifs, and subsequent investigation revealed Gal4p binds unexpectedly to DNA sequences with high densities of its half site (CGG). We confirmed this novel mode of binding through multiple experimental and computational paradigms; we also found most other zinc cluster TFs we tested frequently utilize this binding mode, at 27% of their targets on average. Together, these results demonstrate a novel mode of binding where zinc clusters, the largest class of TFs in yeast, bind DNA sequences with high densities of half sites.

Regulation of ERα-dependent breast cancer metastasis by a miR-29a signaling

Malignant breast cancer (BC) remains incurable mainly due to the cancer cell metastasis, which is mostly related to the status of Estrogen receptor alpha (ERα). However, our understanding of the mechanisms through which ERα regulates cancer cell metastasis remains limited. Here we identified a miR-29a-PTEN-AKT axis as a downstream signaling pathway of ERα governing breast cancer progression and metastasis. Two estrogen response element (ERE) half sites were identified in the promoter and enhancer regions of miR-29a, which mediated transcriptional regulation of miR-29a by ERα. Low level of miR-29a showed association with reduced metastasis and better survival in ERα+ luminal subtype of BC. In contrast, high level of miR-29a was detected in ERα- triple negative breast cancer (TNBC) in association with distant metastasis and poor survival. miR-29a overexpression in BC tumors increased the number of circulating tumor cells and promoted lung metastasis in mice. Targeted knockdown of miR-29a in TNBC cells in vitro or administration of a nanotechnology-based anti-miR-29a delivery in TNBC tumor-bearing mice in vivo suppressed cellular invasion, EMT and lung metastasis. PTEN was identified as a direct target of miR-29a, inducing EMT and metastasis via AKT signaling. A small molecular inhibitor of AKT attenuated miR-29a-induced EMT. These findings demonstrate a novel mechanism responsible for ERα-regulated breast cancer metastasis, and reveal the combination of ERα status and miR-29a levels as a new risk indicator in BC.

Conformational selection in the Cre CBD domain: Insights into intasome assembly.

During site-specific recombination tyrosine recombinases promote scission, insertion, and recombination of specific DNA sequences. The Cre/loxP system from P1 bacteriophage promotes viral DNA circularization after infection and equitable plasmid assortment during cell division. It acts through the formation of a tetramer (intasome) in which Cre monomers are bound in a head-to-tail fashion to a half loxP site, alternating between active and inactive conformations. Despite knowledge of the recombination mechanism and strand exchange order, information regarding target selection and intasome assembly is still missing. We used molecular dynamics simulations (MD) to assess the conformational flexibility of the CBD domain of Cre recombinase. The starting seeds for MD were structures with PDB ID 1q3u (an intasome) and 7rhy (a Cre monomer bound to a loxP half-site); these structures vary in the position of helix A. We simulated four replicas for each system for 5 microseconds in an explicit solvent model (TIP3P) with the software GROMACS using CHARMM36m at 300K and 1 atm. Van der Waals interactions were calculated using a 1.2 nm cutoff and PME for electrostatics, with a 4 fs timestep. Our results show that helix A can switch from an intasome-like to a monomer-like conformation, passing through distinct intermediate and unfolded states. These results suggest that the position of helix A is selected concomitantly with establishing monomer-monomer interactions during intasome assembly. Also, the flexibility of helix A could help to interpret NMR data in which the signals for this helix are missing.We acknowledge the computer resources provided by the LNS del Sureste de México through grant 202101023N, Laboratorio de Supercómputo y Visualización en Paralelo, and LANCAD through grants 99-2021 and 49-2022, and CONACyT (graduate school scholarship 858905, grant INF-2014-02-231504, grant A1-S-11842).

Whole-genome functional characterization of RE1 silencers using a modified massively parallel reporter assay

Both upregulation and downregulation by cis-regulatory elements help modulate precise gene expression. However, our understanding of repressive elements is far more limited than activating elements. To address this gap, we characterized RE1, a group of transcriptional silencers bound by REST, at genome-wide scale using a modified massively parallel reporter assay (MPRAduo). MPRAduo empirically defined a minimal binding strength of REST (REST motif-intrinsic value [m-value]), above which cofactors colocalize and silence transcription. We identified 1,500 human variants that alter RE1 silencing and found that their effect sizes are predictable when they overlap with REST-binding sites above the m-value. Additionally, we demonstrate that non-canonical REST-binding motifs exhibit silencer function only if they precisely align half sites with specific spacer lengths. Our results show mechanistic insights into RE1, which allow us to predict its activity and effect of variants on RE1, providing a paradigm for performing genome-wide functional characterization of transcription-factor-binding sites.

Genome and transcriptome of Chinese medaka (Oryzias sinensis) and its uses as a model fish for evaluating estrogenicity of surface water

Ecological toxicity assessments of contaminants in aquatic environments are of great concern. However, a dilemma in ecological toxicity assessments often arises when linking the effects found in model animals in the laboratory and the phenomena observed in wild fishes in the field due to species differences. Chinese medaka (Oryzias sinensis), widely distributed in East Asia, is a satisfactory model animal to assess aquatic environment in China. Here, we domesticated this species and assembled its genome (814 Mb) using next-generation sequencing (NGS). A total of 21,922 high-confidence genes with 41,306 transcripts were obtained and annotated, and their expression patterns in tissues were determined by RNA-sequencing. Six mostly sensitive biomarker genes, including vtg1, vtg3, vtg6, zp3a.2, zp2l1, and zp2.3 to estrogen exposure were screened and validated in the fish exposed to concentrations of estrone (E1), 17β-estradiol (E2), and estriol (E3) under laboratory condition. Field investigations were then performed to evaluating the gene expression of biomarkers in wild Chinese medaka and levels of E1, E2, and E3 in the fish habitats. It was found that in 40 sampling sites, the biomarker genes were obviously highly expressed in the wild fish from about half sites, and the detection frequencies of E1, E2, and E3, were 97.5%, 42.5%, and 45% with mean concentrations of 82.48, 43.17, 52.69 ng/L, respectively. Correlation analyses of the biomarker gene expressions in the fish with the estrogens levels which were converted to EEQs showed good correlation, indicating that the environmental estrogens and estrogenicity of the surface water might adversely affect wild fishes. Finally, histologic examination of gonads in male wild Chinese medaka was performed and found the presence of intersex in the fish. This study facilitated the uses of Chinese medaka as a model animal for ecotoxicological studies.

RF15 | PMON291 Crystal Structures of Androgen DNA Binding Domain Interacting with its Response Elements (C3(1) ARE and MMTV-GRE)

Abstract Prostate cancer (PCa) is the second leading cancer in the world in men. The major therapeutic target in advanced PCa is the ligand-binding pocket (LBP) of the androgen receptor (AR). The anti-androgens used to treat cancer are binding to this domain and compete with the natural agonist. Over time the cancer grows resistant towards this therapy. Nevertheless, the cancer still typically depends on the AR, indicating other sites of the AR may still serve as drug targets. The DNA binding domain (DBD) is a likely good therapeutic target as it is involved in essential processes such AR dimerization, translocation to the nucleus and binding to the androgen response elements (AREs). However the structure and the DNA binding interactions with AREs are not fully explored yet. Only one crystal structure (pdb: 1R4I) is available. In this structure, the DBD is bound to an artificial direct repeat DNA sequences (ADR3), resulting in an unexpected dimeric head-to-head arrangement. A better understanding on how the AR recognizes and binds to different native DNA sequences which are mainly organized as semi inverted repeats is crucial for rational drug design. Here, we performed protein crystallography of the DBD in complex with various natural ARE sequences, including the mouse mammary tumour virus (MMTV-GRE) motif. Surprisingly, this latter element is still able to be activated by a dimerization deficient AR. Our first crystal structures were hallmarked by a high degree of disorder and appeared to bind both in a head-to-head as a head-to-tail fashion. Rational engineering of the DNA duplexes used for crystallography yielded well diffracting crystals for two different complexes. These two structures were diffracted to a range of 2 to 2.7 Å. Both structures with natural sequences appeared to bind in the head-to-head arrangement including the MMTV-GRE which consist out of semi inverted repeat DNA, whereas the C3(1)ARE contains the canonical fully inverted repeats. The structure reveals a slightly bend arrangement from the previously reported structure. The displacement is most visible at the DNA recognition helix bound to the half site and the so-called lever arm, which positions this helix in this region with a RMSD difference of 1.3 A. This indicates that the structural conformation changes of the protein is driven towards improved DNA-base pair recognition. Indeed the protein is able to make an additional set of non-covalent interactions with the base pairs of MMTV-GRE, leading to higher affinity. Both these extra interactions and conformational change lead to a higher affinity binding of protein-DNA, which seems to overcome the barrier introduced by the dimerization breaking mutations. This interaction surface could be a druggable site for structure-based drug design in the future, targeting AR-DBD dimerization. Presentation: Sunday, June 12, 2022 12:30 p.m. - 12:35 p.m., Monday, June 13, 2022 12:30 p.m. - 2:30 p.m.

Characterization of sequence determinants of enhancer function using natural genetic variation.

Sequence variation in enhancers that control cell-type-specific gene transcription contributes significantly to phenotypic variation within human populations. However, it remains difficult to predict precisely the effect of any given sequence variant on enhancer function due to the complexity of DNA sequence motifs that determine transcription factor (TF) binding to enhancers in their native genomic context. Using F1-hybrid cells derived from crosses between distantly related inbred strains of mice, we identified thousands of enhancers with allele-specific TF binding and/or activity. We find that genetic variants located within the central region of enhancers are most likely to alter TF binding and enhancer activity. We observe that the AP-1 family of TFs (Fos/Jun) are frequently required for binding of TEAD TFs and for enhancer function. However, many sequence variants outside of core motifs for AP-1 and TEAD also impact enhancer function, including sequences flanking core TF motifs and AP-1 half sites. Taken together, these data represent one of the most comprehensive assessments of allele-specific TF binding and enhancer function to date and reveal how sequence changes at enhancers alter their function across evolutionary timescales.

Tackling erosion-accumulation events in a moat sequence from a unique Ottoman memorial place (Szigetv\xe1r, SW Hungary) using 14C and geoarcheological data

One of the most influential rulers of the sixteenth century, Sultan Suleyman I, passed away and was buried temporarily near the fortress of Szigetvár in SW Hungary in 1566. Later, a memorial place was erected on the site in the second half of the sixteenth century. The complex was surrounded by a palisade system and a moat on its northern side. The site was fully destroyed in 1692, and the exact location vanished with time. Recent investigations of historical sources complemented by geophysical, archeological, and geoarcheological investigations managed to identify the location of the site, and probe corings revealed the moat system. This study presents the results of complex chronological, sedimentological, and geochemical investigations done on the sediments accumulated in the moat. Based on geoarcheological data, two major changes could have been noted in the nature of the deposit marking erosion and transportation of soil from the banks of the moat. Elevated concentrations of Fe and K, and high MS values mark the effects of fire on the deposit and accumulation of flue ash. A rise in heavy metals in these horizons is attributable to anthropogenic sources related to the destruction of the site. Chronological data comes from dateable artifacts reposited and 14C dates of charred cereal seeds. A Bayesian age model built using 14C ages constrained by written historical data on site use helped us to determine the age of moat construction and the referred erosion-accumulation events. The older event was dated around 1670, which is in line with historical records of the first siege of Szigetvár. The second event postdates 1684 and thus must correspond to the time of the site’s final siege and later destruction.

Vertical integration of primary care practices with acute hospitals in England and Wales: why, how and so what? Findings from a qualitative, rapid evaluation

ObjectivesTo understand the rationale, implementation and early impact of vertical integration between primary care medical practices and the organisations running acute hospitals in the National Health Service in England and...

Evidence of millet and millet agriculture in the Far East Region of Russia derived from archaeobotanical data and radiocarbon dating

Agriculture based on broomcorn and foxtail millet has been identified as one of the main drivers of population expansion and/or resource and innovation transfer across Neolithic and Bronze Age Eurasia. However, accurate reconstruction of spatio-temporal patterns of millet spread within and outside China remains a challenging issue. Here we use a representative set of 27 millet-based radiocarbon (14C) dates from southern Primorye to reconstruct when millet cultivation became part of hunter-fisher-gatherer subsistence in this vast southeasternmost region of Russia. The spatio-temporal distribution of the 14C data demonstrates the following picture. After the earliest conventionally accepted (although not directly dated) appearance of millet at the Krounovka-1 site in the Suifen (Razdol'naya) River catchment west of Khanka Lake around 3521–3356 BCE (95.4% probability range of calibrated ages of wood charcoal), millet agriculture is registered at the site Gvozdevo-4 located on the southern coastal plains northeast of the mouth of the Tumen (Tumannaya) River in the first half of the 3rd millennium BCE. Several archaeological sites (Novoselishche-4, Bogolyubovka-1, Rettikhovka Geologicheskaya-1, Risovoe-4) with directly dated millet indicate the spread of millet cultivation across the fertile plains around Khanka Lake during the second half of the 3rd millennium BCE. The dates obtained from the Olga-10 site on the eastern coastal plains along the Sea of Japan suggest that millet contributed to the food economy there from the beginning of the 2nd millennium BCE. The presented dataset shows the presence of millet in the north-eastern part of the study region (i.e. at the Glazovka-gorodishche site) in the second half of the 1st millennium BCE. Our dataset demonstrates that millet has been cultivated in southern Primorye since the Late Neolithic, when small-scale agriculture was introduced by Zaisanovskaya culture groups archaeologically documented in the study region and neighbouring regions of China and North Korea. This indicates that millet was an integral part of the subsistence economy of the local populations throughout the entire period under review.

Analysis of the DNA-binding properties of Alx1, an evolutionarily conserved regulator of skeletogenesis in echinoderms

Alx1, a homeodomain-containing transcription factor, is a highly conserved regulator of skeletogenesis in echinoderms. In sea urchins, Alx1 plays a central role in the differentiation of embryonic primary mesenchyme cells (PMCs) and positively regulates the transcription of most biomineralization genes expressed by these cells. The alx1 gene arose via duplication and acquired a skeletogenic function distinct from its paralog (alx4) through the exonization of a 41–amino acid motif (the D2 domain). Alx1 and Alx4 contain glutamine-50 paired-type homeodomains, which interact preferentially with palindromic binding sites in vitro. Chromatin immunoprecipitation sequencing (ChIP-seq) studies have shown, however, that Alx1 binds both to palindromic and half sites in vivo. To address this apparent discrepancy and explore the function of the D2 domain, we used an endogenous cis-regulatory module associated with Sp-mtmmpb, a gene that encodes a PMC-specific metalloprotease, to analyze the DNA-binding properties of Alx1. We find that Alx1 forms dimeric complexes on TAAT-containing half sites by a mechanism distinct from the well-known mechanism of dimerization on palindromic sites. We used transgenic reporter assays to analyze the functional roles of half sites in vivo and demonstrate that two sites with partially redundant functions are essential for the PMC-specific activity of the Sp-mtmmpb cis-regulatory module. Finally, we show that the D2 domain influences the DNA-binding properties of Alx1 in vitro, suggesting that the exonization of this motif may have facilitated the acquisition of new transcriptional targets and consequently a novel developmental function.

Display of the Ancient Religious Bone Cults in the Late Acheulean–Mousterian Art

The relevance of research. One of the most important unsolved problems of cultural studies, religious studies, art history, and history is to determine the time of the origin of religious ideas: that of the beginning of the spiritual evolution of the mankind, which at a certain stage of development begins to master not only the material world but also tries to comprehend the supernatural transcendent reality. The views of scholars regarding the time of the birth of religious beliefs is divided into two opposing points of view. According to one of them, expressed in the works of R. Marett, F. Ratzel, V. Kabo, A. Zubov, religious representations were inherent in the primitive man since the beginning of existence. A serious argument against this version is the fact that art the site of Olduvai culture no object was found that did not have a utilitarian purpose and that could be interpreted as a cult object. However, this fact can be explained by the fact that the rational awareness of the highest supernatural power was preceded by its subconscious (intuitive) sensation, which did not require objectivation in cult objects. Religious ideas were primitive so that they did not need any cult objects. According to other scholars, one can speak of the emergence of religious ideas only from the moment when the cult artefacts appeared; the pre-religious period had lasted until the end of the Mousterian era. However, the discovery of a number of archaeological sites in the second half of the 20th century at the beginning of the 21st century makes it possible to move the beginning of the appearance of Religious beliefs back until the period of the late Acheulean–beginning of Mousterian era.The purpose of the article: to establish the time of the origin and evolution of the earliest religious beliefs associated with the cult of bones, based on the analysis of the most ancient artefacts currently known, which testify to the ritual activities of the primitive man. The considered artefacts lead to the conclusion that the most ancient evidence of the cults of bones belongs to the era of the late Acheulean and Mousterian. Animal bones were among the first objects that the primitive man singled out from the environment as sacred, and endowed with a supernatural ability to revive the lives of animals and humans. Symbolic compositions of bones and signs carved in them became sacred attributes used for magical rites. The first acts of the ritual symbolization marked the emergence of sacred art and magic, which, radically different from the directly useful work, passed into a special plane of connection of men with the supernatural force. The earliest monuments (Torralba, Ambrona, Azykh), which testify to magical actions with bones, date back to about 400–200 thousand years BC. Thus, more than 2 million years passed from the appearance of man (ca. 2.7 million years ago) to the emergence of religious ideas, which required objectification in cult items and the performance of certain rituals. Although it cannot be denied that the intuitive subconscious sense of the supernatural power has been inherent in man since the beginning of his existence, purposefully by cultic magical actions that called on higher powers for help, he began to practice from the period of the late Acheulean. In the Mousterian era, in addition to the cult of bones, the cult of the skull arose as a container of special energy capable of renewing human life. Despite the fact that there are only a few examples of skull burials in the Mousterian period, apart from Mount Circeo, in Zhoukoudian (1929), Ngandonga (1931–1933) and Steingheim (1933), it can be assumed that about 70–50 thousand years ago, along with burials, an undissected body could be another rite of separation of the skull, which as a container of a special vital energy of man was buried in some parts of the caves on piles of bones and stones, just as at about the same time separately buried the skulls of bears in stone boxes and niches in caves of Regurdu, Azykh, Drachenloh, Wildenmannlisloch, and others. Later, with the development of ideas about the soul, the cult of skulls is further developed, based on the realization of the power of the extracorporeal spiritual essence of the revered dead (= ancestors), the concentration of which requires a magical container.

Androgen receptor positively regulates gonadotropin-releasing hormone receptor in pituitary gonadotropes

Within pituitary gonadotropes, the gonadotropin-releasing hormone receptor (GnRHR) receives hypothalamic input from GnRH neurons that is critical for reproduction. Previous studies have suggested that androgens may regulate GnRHR, although the mechanisms remain unknown. In this study, we demonstrated that androgens positively regulate Gnrhr mRNA in mice. We then investigated the effects of androgens and androgen receptor (AR) on Gnrhr promoter activity in immortalized mouse LβT2 cells, which represent mature gonadotropes. We found that AR positively regulates the Gnrhr proximal promoter, and that this effect requires a hormone response element (HRE) half site at -159/-153 relative to the transcription start site. We also identified nonconsensus, full-length HREs at -499/-484 and -159/-144, which are both positively regulated by androgens on a heterologous promoter. Furthermore, AR associates with the Gnrhr promoter in ChIP. Altogether, we report that GnRHR is positively regulated by androgens through recruitment of AR to the Gnrhr proximal promoter.

Differential expression of microRNAs and tRNA fragments mediate the adaptation of the liver fluke Fasciola gigantica to its intermediate snail and definitive mammalian hosts

The tropical liver fluke Fasciola gigantica affects livestock and humans in many Asian countries, large parts of Africa, and parts of Europe. Despite the public health and economic impacts of F. gigantica, understanding of F. gigantica biology and how the complex lifecycle of this liver fluke is transcriptionally regulated remain unknown. Here, we tested the hypothesis that the regulatory small non-coding RNAs (sncRNAs), microRNAs (miRNAs) and tRNA-derived fragments (tRFs) play roles in the adaptation of F. gigantica to its intermediate and definitive hosts. We sequenced sncRNAs of eight lifecycle stages of F. gigantica. In total, 56 miRNAs from 33 conserved families and four Fasciola-specific miRNAs were identified. Expression analysis of miRNAs suggested clear stage-related patterns. By leveraging the existing transcriptomic data, we predicted a miRNA-based regulation of metabolism, transport, growth and developmental processes. Also, by comparing miRNA complement of F. gigantica with that of Fasciola hepatica, we detected a high level of conservation and identified differences in some miRNAs, which can be used to distinguish the two species. Moreover, we found that tRFs at each lifecycle stage were predominantly derived by tRNA-Lys and tRNA-Gly at 5′ half sites, but relatively high expression was related to the buffalo-infecting stages. Taken together, we provided a comprehensive overview of the dynamic transcriptional changes of small RNAs that occur during the developmental stages of F. gigantica. This global analysis of F. gigantica lifecycle stages revealed new roles of miRNAs and tRFs in parasite development and will facilitate future research into understanding of fasciolosis pathobiology.

Generalized hydrodynamics study of the one-dimensional Hubbard model: Stationary clogging and proportionality of spin, charge, and energy currents

In our previous work [Nozawa and Tsunetsugu, Phys. Rev. B 101, 035121 (2020)], we studied the quench dynamics in the one-dimensional Hubbard model based on the generalized hydrodynamics theory for a partitioning protocol and showed the presence of a clogging phenomenon. Clogging is a phenomenon where vanishing charge current coexists with nonzero energy current, and we found it for the initial conditions that the left half of the system is prepared to be half filling at high temperatures with the right half being empty. Clogging occurs at all the sites in the left half and lasts for a time proportional to its distance from the connection point. In this paper, we use various different initial conditions and discuss two issues. The first issue is the possibility of clogging in a stationary state. When the electron density in the right half is initially set nonzero, we found that the left half-filled part expands for various sets of parameters in the initial condition. This means that the clogging phenomenon occurs at all the sites in the long-time stationary state, and we also discuss its origin. In addition, stationary clogging is accompanied by a back current, namely, particle density current flows towards the high-density region. We also found that spin clogging occurs for some initial conditions, i.e., the vanishing spin current coexists with nonzero energy current. The second issue is the proportionality of spin and charge currents. We found two spatiotemporal regions where the current ratio is fixed to a nonzero constant. We numerically studied how the current ratio depends on various initial conditions. We also studied the ratio of charge and energy currents.