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Domain-specific chromatin isolation by RNA purification (dChIRP) identifies interacting partners of functional regions of long noncoding RNAs. Little is known about the functional domain architecture of long noncoding RNAs (lncRNAs) because of a relative paucity of suitable methods to analyze RNA function at a domain level. Here we describe domain-specific chromatin isolation by RNA purification (dChIRP), a scalable technique to dissect pairwise RNA-RNA, RNA-protein and RNA-chromatin interactions at the level of individual RNA domains in living cells. dChIRP of roX1, a lncRNA essential for Drosophila melanogaster X-chromosome dosage compensation, reveals a 'three-fingered hand' ribonucleoprotein topology. Each RNA finger binds chromatin and the male-specific lethal (MSL) protein complex and can individually rescue male lethality in roX -null flies, thus defining a minimal RNA domain for chromosome-wide dosage compensation. dChIRP improves the RNA genomic localization signal by >20-fold relative to previous techniques, and these binding sites are correlated with chromosome conformation data, indicating that most roX-bound loci cluster in a nuclear territory. These results suggest dChIRP can reveal lncRNA architecture and function with high precision and sensitivity.

Confinement of the X chromosome to a territory for dosage compensation is a prime example of how subnuclear compartmentalization is used to regulate transcription at the megabase scale. In Drosophila melanogaster , two sex-specific non-coding RNAs (roX1 and roX2) are transcribed from the X chromosome. They associate with the male-specific lethal (MSL) complex 1 , which acetylates histone H4 lysine 16 and thereby induces an approximately twofold increase in expression of male X-linked genes 2 , 3 . Current models suggest that X-over-autosome specificity is achieved by the recognition of cis -regulatory DNA high-affinity sites (HAS) by the MSL2 subunit 4 , 5 . However, HAS motifs are also found on autosomes, indicating that additional factors must stabilize the association of the MSL complex with the X chromosome. Here we show that the low-complexity C-terminal domain (CTD) of MSL2 renders its recruitment to the X chromosome sensitive to roX non-coding RNAs. roX non-coding RNAs and the MSL2 CTD form a stably condensed state, and functional analyses in Drosophila and mammalian cells show that their interactions are crucial for dosage compensation in vivo. Replacing the CTD of mammalian MSL2 with that from Drosophila and expressing roX in cis is sufficient to nucleate ectopic dosage compensation in mammalian cells. Thus, the condensing nature of roX–MSL2 CTD is the primary determinant for specific compartmentalization of the X chromosome in Drosophila . Dosage compensation in Drosophila involves nucleation of the dosage compensation complex at the X chromosome by MSL2 and the non-coding RNA roX.

Copper slag, a by-product of copper ore and concentrate smelting, is rich in non-ferrous metals; therefore, it has been considered a valuable raw material in recent years. This study aimed to compare the extraction of zinc, copper, and cobalt from two types of copper slag from a dump located near the village of Eliseyna, Bulgaria, which differ in mineralogical composition and chemical content, using indirect bioleaching with a spent medium of Aspergillus niger and Penicillium ochrochloron. Chemical leaching with sulphuric acid revealed that zinc and cobalt existed mainly as an acidic-soluble phase in both types of copper slag. In contrast, it contained 50–75% of the total copper content. Each fungal species was cultivated for one week, and the biomass and the spent medium were separated a week later. Owing to the production of a higher concentration of citric acid, A. niger facilitated more efficient base metal recovery. However, their effective recovery from the acidic-soluble phase required leaching at a 5% pulp density and supplementing the spent medium with sulphuric acid. The temperature played a secondary role. Conclusions: Non-ferrous metal extraction from copper slag exposed to weathering using a spent medium supplemented with sulphuric acid was achieved under milder leaching conditions and with better selectivity. In contrast, slag unaffected by weathering behaved as a refractory due to the worsened results of base metal extraction under similar experimental conditions.

Haploinsufficiency and aneuploidy are two phenomena, where gene dosage alterations cause severe defects ultimately resulting in developmental failures and disease. One remarkable exception is the X chromosome, where copy number differences between sexes are buffered by dosage compensation systems. In Drosophila , the Male-Specific Lethal complex (MSLc) mediates upregulation of the single male X chromosome. The evolutionary origin and conservation of this process orchestrated by MSL2, the only male-specific protein within the fly MSLc, have remained unclear. Here, we report that MSL2, in addition to regulating the X chromosome, targets autosomal genes involved in patterning and morphogenesis. Precise regulation of these genes by MSL2 is required for proper development. This set of dosage-sensitive genes maintains such regulation during evolution, as MSL2 binds and similarly regulates mouse orthologues via Histone H4 lysine 16 acetylation. We propose that this gene-by-gene dosage compensation mechanism was co-opted during evolution for chromosome-wide regulation of the Drosophila male X. In Drosophila the Male-Specific Lethal complex (MSLc) mediates upregulation of the single male X chromosome. Here the authors provide evidence that MSL2 also targets autosomal genes required for proper development and that MSL2 binds and similarly regulates mouse orthologues.

Does Dionaea muscipula, the Venus flytrap, use a particular mechanism to attract animal prey? This question was raised by Charles Darwin 140 years ago, but it remains unanswered. This study tested the hypothesis that Dionaea releases volatile organic compounds (VOCs) to allure prey insects. For this purpose, olfactory choice bioassays were performed to elucidate if Dionaea attracts Drosophila melanogaster. The VOCs emitted by the plant were further analysed by GC-MS and proton transfer reaction-mass spectrometry (PTR-MS). The bioassays documented that Drosophila was strongly attracted by the carnivorous plant. Over 60 VOCs, including terpenes, benzenoids, and aliphatics, were emitted by Dionaea, predominantly in the light. This work further tested whether attraction of animal prey is affected by the nutritional status of the plant. For this purpose, Dionaea plants were fed with insect biomass to improve plant N status. However, although such feeding altered the VOC emission pattern by reducing terpene release, the attraction of Drosophila was not affected. From these results it is concluded that Dionaea attracts insects on the basis of food smell mimicry because the scent released has strong similarity to the bouquet of fruits and plant flowers. Such a volatile blend is emitted to attract insects searching for food to visit the deadly capture organ of the Venus flytrap.

During illumination, the light-sensitive plasma membrane (rhabdomere) of Drosophila photoreceptors undergoes turnover with consequent changes in size and composition. However, the mechanism by which illumination is coupled to rhabdomere turnover remains unclear. We find that photoreceptors contain a light-dependent phospholipase D (PLD) activity. During illumination, loss of PLD resulted in an enhanced reduction in rhabdomere size, accumulation of Rab7 positive, rhodopsin1-containing vesicles (RLVs) in the cell body and reduced rhodopsin protein. These phenotypes were associated with reduced levels of phosphatidic acid, the product of PLD activity and were rescued by reconstitution with catalytically active PLD. In wild-type photoreceptors, during illumination, enhanced PLD activity was sufficient to clear RLVs from the cell body by a process dependent on Arf1-GTP levels and retromer complex function. Thus, during illumination, PLD activity couples endocytosis of RLVs with their recycling to the plasma membrane thus maintaining plasma membrane size and composition. Certain cells in the eye contain a receptor protein known as rhodopsin that enables them to detect light. Rhodopsin is found in distinct patches on the membrane surrounding each of these “photoreceptor” cells and the number of rhodopsin molecules present controls how sensitive the cell is to light. In humans, vitamin A deficiency or genetic defects can decrease the number of rhodopsin molecules on the membrane, leading to difficulty in seeing in dim light. Fruit fly eyes also contain rhodopsin. Exposure to normal levels of light triggers parts of the membranes of fly photoreceptor cells to detach and move into the interior of the cell. These internalized pieces of membrane have two possible fates: they can either be destroyed or recycled back to the cell surface. This membrane turnover adjusts the size of the membrane surrounding the cell and the number of rhodopsin molecules in it to regulate the cell’s sensitivity to light. It is crucial that turnover is tightly regulated in order to maintain the integrity of the cell membrane. However, it is not clear how the process is regulated during light exposure. Thakur et al. set out to address this question in fruit flies. The experiments show that an enzyme called phospholipase D is activated when photoreceptors are exposed to light. Active phospholipase D – which generates a molecule called phosphatidic acid – coordinates the internalization of pieces of membrane with the recycling of rhodopsin back to the cell surface. Thakur et al. generated fly mutants that lacked phospholipase D and in these animals the internalized rhodopsin was not transported back to the cell membrane. This caused the membrane to shrink in size and decreased the number of rhodopsin molecules in it. As a result, the photoreceptor cells became less sensitive to light. The findings of Thakur et al. show that in response to normal levels of light, phospholipase D balances membrane internalization and recycling to maintain the size and rhodopsin composition of the membrane. Future challenges will be to work out exactly how phospholipase D is activated and how phosphatidic acid tunes membrane internalization and recycling.

Sex chromosomes induce potentially deleterious gene expression imbalances that are frequently corrected by dosage compensation (DC). Three distinct molecular strategies to achieve DC have been previously described in nematodes, fruit flies, and mammals. Is this a consequence of distinct genomes, functional or ecological constraints, or random initial commitment to an evolutionary trajectory? Here, we study DC in the malaria mosquito Anopheles gambiae . The Anopheles and Drosophila X chromosomes evolved independently but share a high degree of homology. We find that Anopheles achieves DC by a mechanism distinct from the Drosophila MSL complex–histone H4 lysine 16 acetylation pathway. CRISPR knockout of Anopheles msl-2 leads to embryonic lethality in both sexes. Transcriptome analyses indicate that this phenotype is not a consequence of defective X chromosome DC. By immunofluorescence and ChIP, H4K16ac does not preferentially enrich on the male X. Instead, the mosquito MSL pathway regulates conserved developmental genes. We conclude that a novel mechanism confers X chromosome up-regulation in Anopheles . Our findings highlight the pluralism of gene-dosage buffering mechanisms even under similar genomic and functional constraints.

This article presents the preliminary results of several consecutive studies conducted in the period 2021–2024. The area of the Ludogorsko Plateau is characterised by one of the highest concentrations of Late Bronze Age finds discovered in present-day Bulgaria. Unfortunately, more than 100 years after the first discoveries, no large-scale studies focusing on the period of the 2nd millenium BC have been carried out. The fieldwork strategy included combination of various research methods – from remote and non-destructive methods (LiDAR, geophysics, field surveys) to conventional archaeological excavations (trenches and long-term excavations over a larger area) for the sites selected for these studies.The archaeological site in the locality of Yurtluka near the village of Kamenovo was registered during the first campaign (2021). Its identification as promising for future more detailed fieldwork led to the successive implementation of large-scale geomagnetic surveys and the first regular excavations in 2023.The results presented are diverse and allow analyses and interpretations of various research questions relating to the settlement environment, the internal organisation of the site, the characteristics of the pottery assemblage and the main groups of artefacts. Initial hypotheses about chronology, possible supra-regional contacts and interactions in this part of the Ludogorsko Plateau during the Late Bronze Age are also put forward.

The NSL complex is a transcriptional activator. Germline-specific knockdown of NSL complex subunits NSL1, NSL2, and NSL3 results in reduced piRNA production from a subset of bidirectional piRNA clusters, accompanied by widespread transposon derepression. The piRNAs most transcriptionally affected by NSL2 and NSL1 RNAi map to telomeric piRNA clusters. At the chromatin level, these piRNA clusters also show decreased levels of H3K9me3, HP1a, and Rhino after NSL2 depletion. Using NSL2 ChIP-seq in ovaries, we found that this protein specifically binds promoters of telomeric transposons HeT-A , TAHRE , and TART . Germline-specific depletion of NSL2 also led to a reduction in nuclear Piwi in nurse cells. Our findings thereby support a role for the NSL complex in promoting the transcription of piRNA precursors from telomeric piRNA clusters and in regulating Piwi levels in the Drosophila female germline.

The paper presents evidence of Roman marble production in the Balkan region, specifically from the south-eastern Rhodope Mountain area (modern Bulgaria) and Armira. Although the Roman marble trade and production in antiquity are well known in Prokonnesos, Thasos, and several other production sites, marble deposits from inland Thrace have received far less attention. In 2018–2019, a systematic survey of south-eastern Bulgaria (Roman Thrace) was carried out by our team in collaboration with the National Archaeological Institute with Museum in Bulgaria. White marble quarries and outcrops were investigated in situ with the goal of characterizing the macroscopic qualities of the stone. Quarry samples were collected and analyzed through various techniques—petrography, isotopic, and chemical analyses—and compared with the architectural decorative marble and artifacts from the Roman villa at Armira. We demonstrate that the geochemical and petrographic features of these samples indicate a marble provenance restricted to a few selected sources. We conclude that the local marble from the Armira and Kamilski Dol quarries was widely used for the complete architectural program of the Roman villa of Armira.