A universal system for boosting gene expression in eukaryotic cell-lines.

We demonstrate a transcriptional regulatory design algorithm that can boost expression in yeast and mammalian cell lines. The system consists of a simplified transcriptional architecture composed of a minimal core promoter and a synthetic upstream regulatory region (sURS) composed of up to three motifs selected from a list of 41 motifs conserved in the eukaryotic lineage. The sURS system was first characterized using an oligo-library containing 189,990 variants.

Wikipedia as a tool for contemporary history of science: A case study on CRISPR.

Rapid developments and methodological divides hinder the study of how scientific knowledge accumulates, consolidates and transfers to the public sphere. Our work proposes using Wikipedia, the online encyclopedia, as a historiographical source for contemporary science. We chose the high-profile field of gene editing as our test case, performing a historical analysis of the English-language Wikipedia articles on CRISPR.

Real World Characterization of Chronic Pain, Success Rates and Implant Rates: Evidence from a Digital Health Platform of Patients Undergoing Spinal Cord Stimulation Evaluations.

Spinal cord stimulation is an effective treatment for those experiencing chronic back and leg pain but requires a temporary evaluation period (SCSeval) before permanent implantation. We present real-world data from 7,000 patients who underwent SCSeval while utilizing a mobile digital health platform for education, feedback, and outcomes collection during their surgical journey. We analyzed preoperative patient demographics, characterized patient pain profiles using the patient-reported outcomes measurement information system-29 surveys, and calculated the rates of conversion from temporary to permanent spinal cord stimulation (SCS) implantation.

What's on the horizon for community-based conservation? Emerging threats and opportunities.

Community-based conservation can support livelihoods and biodiversity, while reinforcing local and Indigenous values, cultures, and institutions. Its delivery can help address cross-cutting global challenges, such as climate change, conservation, poverty, and food security. Therefore, understanding trends in community-based conservation is pertinent to setting and implementing global goals.

Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes.

Liquid-solid transition, also known as gelation, is a specific form of phase separation in which molecules cross-link to form a highly interconnected compartment with solid - like dynamical properties. Here, we utilize RNA hairpin coat-protein binding sites to form synthetic RNA based gel-like granules via liquid-solid phase transition. We show both in-vitro and in-vivo that hairpin containing synthetic long non-coding RNA (slncRNA) molecules granulate into bright localized puncta.

Molecular and experimental tools to design synthetic enhancers.

Understanding the grammar of enhancers and how they regulate gene expression is key for both basic research and for the pharma and biotech industries. The design and characterization of synthetic enhancers can expand the known regulatory space. This is achieved by the utilization of DNA Oligo Libraries (OLs), which facilitates screening of as many as millions of synthetic enhancer variants simultaneously.

A Cell-Free Assay for Rapid Screening of Inhibitors of hACE2-Receptor-SARS-CoV-2-Spike Binding.

We present a cell-free assay for rapid screening of candidate inhibitors of protein binding, focusing on inhibition of the interaction between the SARS-CoV-2 Spike receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (hACE2). The assay has two components: fluorescent polystyrene particles covalently coated with RBD, termed virion-particles (v-particles), and fluorescently labeled hACE2 (hACE2F) that binds the v-particles. When incubated with an inhibitor, v-particle-hACE2F binding is diminished, resulting in a reduction in the fluorescent signal of bound hACE2F relative to the noninhibitor control, which can be measured via flow cytometry or fluorescence microscopy.

An Oligo-Library-Based Approach for Mapping DNA-DNA Triplex Interactions .

We present Triplex-seq, a deep-sequencing method that systematically maps the interaction space between an oligo library of ssDNA triplex-forming oligos (TFOs) and a particular dsDNA triplex target site (TTS). We demonstrate the method using a randomized oligo library comprising 67 million variants, with five TTSs that differ in guanine (G) content, at two different buffer conditions, denoted pH 5 and pH 7. Our results show that G-rich triplexes form at both pH 5 and pH 7, with the pH 5 set being more stable, indicating that there is a subset of TFOs that form triplexes only at pH 5.

Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes.

We apply an oligo-library and machine learning-approach to characterize the sequence and structural determinants of binding of the phage coat proteins (CPs) of bacteriophages MS2 (MCP), PP7 (PCP), and Qβ (QCP) to RNA. Using the oligo library, we generate thousands of candidate binding sites for each CP, and screen for binding using a high-throughput dose-response Sort-seq assay (iSort-seq). We then apply a neural network to expand this space of binding sites, which allowed us to identify the critical structural and sequence features for binding of each CP.

Evaluation of delay in time to adjuvant chemotherapy after HIPEC and its impact on oncological outcome in advanced epithelial ovarian cancer.

Obejectives: Optimal cytoreductive surgery (CRS), followed by adjuvant chemotherapy, is a major predictor of oncological outcome in patients with advanced epithelial ovarian carcinoma (EOC). It is not clear if a delayed start of adjuvant chemotherapy negatively impacts on the oncological outcome.

Methods: Prospective registry study on 75 patients treated with CRS and hyperthermic intraperitoneal chemotherapy (HIPEC).

Oculomotor inhibition precedes temporally expected auditory targets.

Eye movements are inhibited prior to the onset of temporally-predictable visual targets. This oculomotor inhibition effect could be considered a marker for the formation of temporal expectations and the allocation of temporal attention in the visual domain. Here we show that eye movements are also inhibited before predictable auditory targets.

Author Correction: Data storage in DNA with fewer synthesis cycles using composite DNA letters.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Data storage in DNA with fewer synthesis cycles using composite DNA letters.

The density and long-term stability of DNA make it an appealing storage medium, particularly for long-term data archiving. Existing DNA storage technologies involve the synthesis and sequencing of multiple nominally identical molecules in parallel, resulting in information redundancy. We report the development of encoding and decoding methods that exploit this redundancy using composite DNA letters.

An Assay for Quantifying Protein-RNA Binding in Bacteria.

In the initiation step of protein translation, the ribosome binds to the initiation region of the mRNA. Translation initiation can be blocked by binding of an RNA binding protein (RBP) to the initiation region of the mRNA, which interferes with ribosome binding. In the presented method, we utilize this blocking phenomenon to quantify the binding affinity of RBPs to their cognate and non-cognate binding sites.

Synthetic 5' UTRs Can Either Up- or Downregulate Expression upon RNA-Binding Protein Binding.

The construction of complex gene-regulatory networks requires both inhibitory and upregulatory modules. However, the vast majority of RNA-based regulatory "parts" are inhibitory. Using a synthetic biology approach combined with SHAPE-seq, we explored the regulatory effect of RNA-binding protein (RBP)-RNA interactions in bacterial 5' UTRs.

Designing Bacterial Chemotactic Receptors Guided by Photonic Femtoliter Well Arrays for Quantifiable, Label-Free Measurement of Bacterial Chemotaxis.

Whole cell bioreporters, such as bacterial cells, can be used for environmental and clinical sensing of specific analytes. However, the current methods implemented to observe such bioreporters in the form of chemotactic responses heavily rely on microscope analysis, fluorescent labels, and hard-to-scale microfluidic devices. Herein, we demonstrate that chemotaxis can be detected within minutes using intrinsic optical measurements of silicon femtoliter well arrays (FMAs).

Transient and sustained effects of stimulus properties on the generation of microsaccades.

Saccades shift the gaze rapidly every few hundred milliseconds from one fixated location to the next, producing a flow of visual input into the visual system even in the absence of changes in the environment. During fixation, small saccades called microsaccades are produced 1-3 times per second, generating a flow of visual input. The characteristics of this visual flow are determined by the timings of the saccades and by the characteristics of the visual stimuli on which they are performed.

An in Vivo Binding Assay for RNA-Binding Proteins Based on Repression of a Reporter Gene.

We study translation repression in bacteria by engineering a regulatory circuit that functions as a binding assay for RNA binding proteins (RBP) in vivo. We do so by inducing expression of a fluorescent protein-RBP chimera, together with encoding its binding site at various positions within the ribosomal initiation region (+11-13 nt from the AUG) of a reporter module. We show that when bound by their cognate RBPs, the phage coat proteins for PP7 (PCP) and Qβ (QCP), strong repression is observed for all hairpin positions within the initiation region.

Oculomotor inhibition reflects temporal expectations.

The accurate extraction of signals out of noisy environments is a major challenge of the perceptual system. Forming temporal expectations and continuously matching them with perceptual input can facilitate this process. In humans, temporal expectations are typically assessed using behavioral measures, which provide only retrospective but no real-time estimates during target anticipation, or by using electrophysiological measures, which require extensive preprocessing and are difficult to interpret.

Oculomotor behavior during non-visual tasks: The role of visual saliency.

Background: During visual exploration or free-view, gaze positioning is largely determined by the tendency to maximize visual saliency: more salient locations are more likely to be fixated. However, when visual input is completely irrelevant for performance, such as with non-visual tasks, this saliency maximization strategy may be less advantageous and potentially even disruptive for task-performance. Here, we examined whether visual saliency remains a strong driving force in determining gaze positions even in non-visual tasks.

Participatory development of incentives to coexist with jaguars and pumas.

Reducing costs and increasing benefits for rural communities coexisting with large carnivores is necessary for conservation of jaguar (Panthera onca) and puma (Puma concolor). To design acceptable incentives, stakeholders must be involved in the process. We conducted an innovative, structured, group communication process based on a Delphi technique as a template for identifying potential incentives.

A Synthetic Oligo Library and Sequencing Approach Reveals an Insulation Mechanism Encoded within Bacterial σ Promoters.

We use an oligonucleotide library of >10,000 variants to identify an insulation mechanism encoded within a subset of σ promoters. Insulation manifests itself as reduced protein expression for a downstream gene that is expressed by transcriptional readthrough. It is strongly associated with the presence of short CT-rich motifs (3-5 bp), positioned within 25 bp upstream of the Shine-Dalgarno (SD) motif of the silenced gene.

Temporal dynamics of saccades explained by a self-paced process.

Sensory organs are thought to sample the environment rhythmically thereby providing periodic perceptual input. Whisking and sniffing are governed by oscillators which impose rhythms on the motor-control of sensory acquisition and consequently on sensory input. Saccadic eye movements are the main visual sampling mechanism in primates, and were suggested to constitute part of such a rhythmic exploration system.

A Looping-Based Model for Quenching Repression.

We model the regulatory role of proteins bound to looped DNA using a simulation in which dsDNA is represented as a self-avoiding chain, and proteins as spherical protrusions. We simulate long self-avoiding chains using a sequential importance sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chain's termini reduces the probability of looping, even for chains much longer than the protrusion-chain-terminus distance.