The spatial biology of transcription and translation in rapidly growing Escherichia coli.

Single-molecule fluorescence provides high resolution spatial distributions of ribosomes and RNA polymerase (RNAP) in live, rapidly growing Escherichia coli. Ribosomes are more strongly segregated from the nucleoids (chromosomal DNA) than previous widefield fluorescence studies suggested. While most transcription may be co-translational, the evidence indicates that most translation occurs on free mRNA copies that have diffused from the nucleoids to a ribosome-rich region. Analysis of time-resolved images of the nucleoid spatial distribution after treatment with the transcription-halting drug rifampicin and the translation-halting drug chloramphenicol shows that both drugs cause nucleoid contraction on the 0-3 min timescale. This is consistent with the transertion hypothesis. We suggest that the longer-term (20-30 min) nucleoid expansion after Rif treatment arises from conversion of 70S-polysomes to 30S and 50S subunits, which readily penetrate the nucleoids. Monte Carlo simulations of a polymer bead model built to mimic the chromosomal DNA and ribosomes (either 70S-polysomes or 30S and 50S subunits) explain spatial segregation or mixing of ribosomes and nucleoids in terms of excluded volume and entropic effects alone. A comprehensive model of the transcription-translation-transertion system incorporates this new information about the spatial organization of the E. coli cytoplasm. We propose that transertion, which radially expands the nucleoids, is essential for recycling of 30S and 50S subunits from ribosome-rich regions back into the nucleoids. There they initiate co-transcriptional translation, which is an important mechanism for maintaining RNAP forward progress and protecting the nascent mRNA chain. Segregation of 70S-polysomes from the nucleoid may facilitate rapid growth by shortening the search time for ribosomes to find free mRNA concentrated outside the nucleoid and the search time for RNAP concentrated within the nucleoid to find transcription initiation sites

Sizable suppression of magnon Hall effect by magnon damping in Cr2_2Ge2_2Te6_6

Two-dimensional (2D) Heisenberg honeycomb ferromagnets are expected to have interesting topological magnon effects as their magnon dispersion can have Dirac points. The Dirac points are gapped with finite second nearest neighbor Dzyaloshinskii-Moriya interaction, providing nontrivial Berry curvature with finite magnon Hall effect. Yet, it is unknown how the topological properties are affected by magnon damping. We report the thermal Hall effect in Cr$_2$Ge$_2$Te$_6$, an insulating 2D honeycomb ferromagnet with a large Dirac magnon gap and significant magnon damping. Interestingly, the thermal Hall conductivity in Cr$_2$Ge$_2$Te$_6$ shows the coexisting phonon and magnon contributions. Using an empirical two-component model, we successfully estimate the magnon contribution separate from the phonon part, revealing that the magnon Hall conductivity was 20 times smaller than the theoretical calculation. Finally, we suggest that such considerable suppression in the magnon Hall conductivity is due to the magnon damping effect in Cr$_2$Ge$_2$Te$_6$.Comment: 15 pages, 3 figures. Accepted for publication in Phys. Rev.

Band gap opening by two-dimensional manifestation of Peierls instability in graphene

Using first-principles calculations of graphene having high-symmetry distortion or defects, we investigate band gap opening by chiral symmetry breaking, or intervalley mixing, in graphene and show an intuitive picture of understanding the gap opening in terms of local bonding and antibonding hybridizations. We identify that the gap opening by chiral symmetry breaking in honeycomb lattices is an ideal two-dimensional (2D) extension of the Peierls metal-insulator transition in 1D linear lattices. We show that the spontaneous Kekule distortion, a 2D version of the Peierls distortion, takes place in biaxially strained graphene, leading to structural failure. We also show that the gap opening in graphene antidots and armchair nanoribbons, which has been attributed usually to quantum confinement effects, can be understood with the chiral symmetry breaking

RNA Granules Hitchhike on Lysosomes for Long-Distance Transport, Using Annexin A11 as a Molecular Tether

Long-distance RNA transport enables local protein synthesis at metabolicallyactive sites distant from the nucleus. This process ensures an appropriate spatial organization of proteins, vital to polarized cells such as neurons. Here, we present a mechanism for RNA transport in which RNA granules “hitchhike” on moving lysosomes. In vitro biophysical modeling, live-cell microscopy, and unbiased proximity labeling proteomics reveal that annexin A11 (ANXA11), an RNA granule-associated phosphoinositide-binding protein, acts as a molecular tether between RNA granules and lysosomes. ANXA11 possesses an N-terminal low complexity domain, facilitating its phase separation into membraneless RNA granules, and a C-terminal membrane binding domain, enabling interactions with lysosomes. RNA granule transport requires ANXA11, and amyotrophic lateral sclerosis (ALS) mutations impair RNA granule transport in neurons by disrupting their interactions with lysosomes. Thus, ANXA11 mediates neuronal RNA transport by tethering RNA granules to actively-transported lysosomes, performing a critical cellular function that is disrupted in ALS

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P < 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

A Study on Indexing Efficiency and Retrieval Accuracy for Author Name Search of Academic Papers

Abstract: Most academic information has its creator, that is, a subject who has created the information. The subject can be an individual, a group, or an institution, and can be a nation depending on the nature of the relevant information. Most web data are composed of a title, an author, and contents. A paper which is under the academic information category has metadata including a title, an author, keyword, abstract, data about publication, place of publication, ISSN, and the like. A patent has metadata including the title, an applicant, an inventor, an attorney, IPC, number of application, and claims of the invention. Most web-based academic information services enable users to search the information by processing the meta-information. An important element is to search information by using the author field which corresponds to a personal name. This study suggests a method of efficient indexing and using the adjacent operation result ranking algorithm to which phrase search-based boosting elements are applied, and thus improving the accuracy of the search results of author name. This method can be effectively applied to providing accurate search results in the academic information services

Seeking Mental Health Support Among College Students in Video-Based Social Media: Content and Statistical Analysis of YouTube Videos

BackgroundMental health is a highly stigmatized disease, especially for young people. Due to its free, accessible format, college students increasingly use video-based social media for many aspects of information needs, including how-to tips, career, or health-related needs. The accessibility of video-based social media brings potential in supporting stigmatized contexts, such as college students’ mental health. Understanding which kinds of videos about college students’ mental health have increased viewer engagement will help build a foundation for exploring this potential. Little research has been done to identify video types systematically, how they have changed over time, and their associations on viewer engagement both short term and long term. ObjectiveThis study aims to identify strategies for using video-based social media to combat stigmatized diseases, such as mental health, among college students. We identify who, with what perspective, purpose, and content, makes up the videos available on social media (ie, YouTube) about college students’ mental health and how these factors associate with viewer engagement. We then identify effective strategies for designing video-based social media content for supporting college students’ mental health. MethodsWe performed inductive content analysis to identify different types of YouTube videos concerning college students’ mental health (N=452) according to video attributes, including poster, perspective, and purpose. Time analysis showed how video types have changed over time. Fisher’s exact test was used to examine the relationships between video attributes. The Mann-Whitney U test was used to test the association between video types and viewer engagement. Lastly, we investigated the difference in viewer engagement across time between two major types of videos (ie, individuals’ storytelling and organization’s informational videos). ResultsTime trend analysis showed a notable increase in the number of (1) videos by individuals, (2) videos that represent students’ perspectives, and (3) videos that share stories and experiential knowledge over the recent years. Fisher’s exact test found all video attributes (ie, poster, perspective, and purpose) are significantly correlated with each other. In addition, the Mann-Whitney U test found that poster (individual vs organization) and purpose (storytelling vs sharing information) type has a significant association with viewer engagement (P<.001). Lastly, individuals’ storytelling videos had a greater engagement in the short term and the long term. ConclusionsThe study shows that YouTube videos on college students’ mental health can be well differentiated by the types of posters and the purpose of the videos. Taken together, the videos where individuals share their personal stories, as well as experiential knowledge (ie, tips and advice), engaged more viewers in both the short term and long term. Individuals’ videos on YouTube showed the potential to support college students' mental health in unique ways, such as providing social support, validating experience, and sharing the positive experience of help-seeking

A Case Study on Distresses of Concrete Pavements Supported on a Retaining Wall

Embankments and retaining walls are integral parts of the bridge system and provide a smooth transition from lower elevations (i.e., roadways) to higher elevations (i.e., bridge decks). Performances of pavement structures supported on embankments or retaining walls are directly related to their conditions. This paper presents a comprehensive case study of the evaluation of pavement structures supported on an in-service mechanically stabilized earth (MSE) wall that showed significant distresses, such as lane separation, faulting, lane settlement, and tilting of the MSE wall. The conditions of the pavement structures were evaluated via visual observations, falling weight deflectometer (FWD) tests, and coring through pavement structures. The conditions of the MSE wall were evaluated through dynamic cone penetrometer (DCP) tests, cone penetration tests (CPTs), LiDAR surveys, and soil borings. Detailed analysis of the data obtained in this study provides valuable insights into potential distress mechanisms

Antimicrobial peptides and their MICs for <i>E</i>. <i>coli</i> MG1655 in aerobic growth vs anaerobic fermentation in EZRDM at 30°C.

<p>Antimicrobial peptides and their MICs for <i>E</i>. <i>coli</i> MG1655 in aerobic growth vs anaerobic fermentation in EZRDM at 30°C.</p