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Although gene expression is tightly controlled at both the RNA and protein levels, the quantitative contribution of each step, especially during dynamic responses, remains largely unknown. Indeed, there has been much debate whether changes in RNA level contribute substantially to protein-level regulation. Jovanovic et al. built a genome-scale model of the temporal dynamics of differential protein expression during the stimulation of immunological dendritic cells (see the Perspective by Li and Biggin). Newly stimulated functions involved the up-regulation of specific RNAs and concomitant increases in the levels of the proteins they encode, whereas housekeeping functions were regulated posttranscriptionally at the protein level. Science , this issue 10.1126/science.1259038 ; see also p. 1066 Levels of “housekeeping” proteins are maintained directly, but those of immune response proteins depend on more transcription. [Also see Perspective by Li and Biggin ] Protein expression is regulated by the production and degradation of messenger RNAs (mRNAs) and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics so as to build a quantitative genomic model of the differential regulation of gene expression in lipopolysaccharide-stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for more than half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction for newly activated cellular functions and by protein life-cycle changes for remodeling of preexisting functions.

Beeswax is one of the most important products for the well-being of bee colonies. The wax glands of young worker bees produce beeswax, which serves as a building material for honeycomb construction. Beekeepers using hives with mobile frames mainly utilize local beeswax to make foundations. Any paraffin addition represents adulteration, resulting in a high degree of contamination. During the preparation of re-used beeswax, losses during the process may instigate producers to add cheaper, wax-like substances like paraffin and tallow. This article presents a systematic investigation of the quality of beeswax foundation from six major producers in Vojvodina, Serbia, by applying the classic analytical procedure for the determination of selected physicochemical parameters and instrumental gas chromatography coupled with mass spectrometry (GC–MS) and Fourier transform infrared attenuated total reflection (FTIR–ATR) spectroscopy techniques. FTIR–ATR detected possible paraffin and beef tallow in 72 foundation sheet samples. This technique was complemented with GC–MS. This analysis revealed that paraffin content ranged between 19.75 and 85.68%, while no tallow was detected over the two-year period. Two sheets from each manufacturer were placed into wired Langstroth–Ruth frames and placed in beehives. The construction, based on built cells, was monitored every 24 h. Evaluating newly inserted sheets proved that without quality nectar, there is no intensive building, regardless of adulteration.

Previous studies of ideological attitudes show gender differences in ideological self-positioning on the left-right scale, where it is concluded that women are more inclined to left-wing and progressive ideas? they more often identify themselves with the center-left compared to men. This phenomenon is called the modern gender gap. This paper examines whether this shift of women towards the center left, which was recorded in the countries of Western Europe, also exists in Serbia. The work uses the databases of public opinion research (1990-2024), owned by the Institute of Social Sciences, and international research conducted in Serbia. Examining the ideological positioning of men and women in Serbia over the past three decades can provide valuable insights into both the nature of the gender gap and the importance of self-centeredness in the post-socialist context. The results of the research in Serbia show that the predominant self-positioning of women in the position of the center left (only average values are considered) does not result primarily from their stronger connection with the left, but rather represents a combination of a lower tendency to position themselves on the right and a greater tendency towards the center. Additional analyses of gender differences showed that choosing the center on the scale left and right can be an expression of insecurity and the absence of clear attitudes, which opens up space for further examination of the motives of women to choose a centrist position on the scale.

Targeted selection-based genome-editing approaches have enabled many fundamental discoveries and are used routinely with high precision. We found, however, that replacement of DBP1 with a common selection cassette in budding yeast led to reduced expression and function for the adjacent gene, MRP51 , despite all MRP51 coding and regulatory sequences remaining intact. Cassette-induced repression of MRP51 drove all mutant phenotypes detected in cells deleted for DBP1 . This behavior resembled the ‘neighboring gene effect’ (NGE), a phenomenon of unknown mechanism whereby cassette insertion at one locus reduces the expression of a neighboring gene. Here, we leveraged strong off-target mutant phenotypes resulting from cassette replacement of DBP1 to provide mechanistic insight into the NGE. We found that the inherent bidirectionality of promoters, including those in expression cassettes, drives a divergent transcript that represses MRP51 through combined transcriptional interference and translational repression mediated by production of a long undecoded transcript isoform (LUTI). Divergent transcript production driving this off-target effect is general to yeast expression cassettes and occurs ubiquitously with insertion. Despite this, off-target effects are often naturally prevented by local sequence features, such as those that terminate divergent transcripts between the site of cassette insertion and the neighboring gene. Thus, cassette-induced off-target effects can be eliminated by the insertion of transcription terminator sequences into the cassette, flanking the promoter. Because the driving features of this off-target effect are broadly conserved, our study suggests it should be considered in the design and interpretation of experiments using integrated expression cassettes in other eukaryotic systems, including human cells.

In the last decade, increased availability of 3d printers and laser cutters has led to development of specialized market for producing models as souvenirs and personalized gifts. One type of such models are city scale-models. The topic of this research deals with the examination of various laser engraving and laser cutting techniques, as well as the application of 3d printing in the production of specialized city scale-models. The aim of the research is to find the most efficient way of realising this project while fulfilling the following criteria: production time, quality of the final result (need for additional processing) and total production costs. Results of this research are successfully fabricated city scale-models and a tabular overview containing data on the basis of which the best approach can be determined, in relation to given predispositions.

Ribosomes are RNA-protein complexes essential for protein synthesis and quality control. Traditional methods for ribosome isolation are labor-intensive, expensive, and require a substantial amount of biological material. In contrast, our method, RNA affinity purification using poly-lysine (RAPPL), provides a rapid, simple, and cost-effective alternative applicable to various species and types of starting material (cell lysates, whole cells, organs, or whole organisms). It is also compatible with traditional isolation techniques. Here, we describe the use of RAPPL for rapid isolation, functional screening, and structural analysis of ribosomes and associated factors. We also demonstrate the application of RAPPL in investigating ribosome-associated resistance mechanisms in uropathogeni c Escherichia coli samples and generating a 2.7-Å cryoEM ribosome structure from Cryptococcus neoformans . By significantly reducing the amount of the starting biological material and the time required for isolation, RAPPL has the potential to facilitate the study of ribosomal function, interactions, and antibiotic resistance and provide a versatile platform for academic, clinical, and industrial research. Here, the authors present a method to rapidly isolate actively translating ribosomes in a time- and cost-effective manner using poly-lysine. The method is compatible with a wide variety of cell and tissue types and can be used for mass spectrometry, cryoEM, and in vitro translation assays.

A protein’s molecular interactions and post-translational modifications (PTMs), such as phosphorylation, can be co-dependent and reciprocally co-regulate each other. Although this interplay is central for many biological processes, a systematic method to simultaneously study assembly states and PTMs from the same sample is critically missing. Here, we introduce SEC-MX (Size Exclusion Chromatography fractions MultipleXed), a global quantitative method combining Size Exclusion Chromatography and PTM-enrichment for simultaneous characterization of PTMs and assembly states. SEC-MX enhances throughput, allows phosphopeptide enrichment, and facilitates quantitative differential comparisons between biological conditions. Conducting SEC-MX on HEK293 and HCT116 cells, we generate a proof-of-concept dataset, mapping thousands of phosphopeptides and their assembly states. Our analysis reveals intricate relationships between phosphorylation events and assembly states and generates testable hypotheses for follow-up studies. Overall, we establish SEC-MX as a valuable tool for exploring protein functions and regulation beyond abundance changes. SEC-MX enables simultaneous quantitative differential analysis of protein assembly states and post-translational modifications, shedding light on their complex interplay and on protein regulation beyond abundance measurements.

Diverse epigenetic regulatory mechanisms ensure and modulate cellular diversity. The histone 3 lysine 9 me3 (H3K9me3) post-translational modification participates in silencing lineage-inappropriate genes by restricting access of transcription factors and other regulatory proteins to genes that control cell fate. Mouse olfactory sensory neurons (OSNs) select one olfactory receptor (OR) gene out of 2600 possibilities. This monoallelic and stochastic OR choice occurs as OSNs differentiate and undergo dramatic changes in nuclear architecture. OR genes from different chromosomes converge into specialized nuclear bodies and chromatin compartments, as H3K9me3 and chromatin binding proteins including heterochromatin protein 1 (HP1) are incorporated. In this work, we have uncovered an unexpected role for HP1β in OR choice and neuronal identity that cannot be rescued by HP1α in vivo. With the use of a conditional knock-in mouse model, that after CRE expression replaces HP1β with HP1α, we observe changes in H3K9me3 levels and DNA accessibility over OR gene clusters. These changes alter the expression patterns that partition the mouse olfactory epithelium into five OR expression zones, which results in a reduced OR repertoire that leads to a loss of olfactory sensory neuron diversity. We propose that HP1β modulates the competition of OR promoters for enhancers to promote receptor diversity by establishing repression gradients in a zonal fashion.

With an increasing interest in fabricating complex structures in architectural design, the concept of porosity has become a vital topic, opening up new avenues for tectonic thinking and functional demands in architecture. Porous structures typically consist of minute interstices or modular structural grids that allow fluids to pass through and are typically present on a micro scale. By adopting a biomimetic approach, which moves from the micro to the macro scale, the application of digital tools has enabled the design of functional building elements. For example, the 30 St Mary Axe tower by Foster and Partners imitates the shape and porosity of a Venus Flower Basket Sponge, resulting in enhanced endurance capabilities. Furthermore, porous structures can improve the building’s thermal, light, and air circulation conditions. However, porous structures have a highly complex topology that poses a challenge for the fabrication process, and is primarily limited to 3D printing and CNC milling manufacturing approaches, with the addition of casting and chemical processes depending on the material. In this research, we propose a novel design and manufacturing approach for porous structure fabrication that uses a hot knife tool with an industrial robot to cut expanded polystyrene materials. This approach offers a faster and more efficient way to fabricate porous structures than additive or milling techniques, with an integrated design approach that enables a range of design scenarios to be explored. Additionally, our method provides hands-on experience and practical testing of a large-scale prototype.

The regulation of mRNA translation is a fundamental aspect of gene expression control. Although cells have precise mechanisms to regulate each step of translation, the primary regulatory events occur during initiation. Among the transcripts subject to tight translational control are those containing a terminal oligopyrimidine (TOP) motif. In mammals, TOP mRNAs predominantly encode components of the translational machinery, including all ribosomal proteins and translation factors. La-related protein 1 (LARP1) has emerged as a key regulator of TOP mRNAs. LARP1 binds directly to the TOP motif, modulating the stability and translational activity of these transcripts. However, the molecular mechanism by which LARP1 controls translation initiation remains unresolved, with evidence supporting both translational repression and activation. Here, we used single-particle cryo-electron microscopy (cryo-EM) to identify the precise binding site of LARP1 at the mRNA entry channel in the 40S small ribosome subunit. Strikingly, the position of LARP1 within the mRNA channel is sterically incompatible with active translation, as it would clash with both incoming mRNA and initiator tRNAiMet during translation initiation. These findings support a model in which non-translating ribosomes associate with LARP1-bound TOP mRNAs, linking TOP mRNA translation to ribosome availability. This interaction may constitute a ribosome- autoregulatory feedback loop that adjusts ribosome biogenesis in response to cellular demands.