bluuebunny/crossref_metadata_2025 huggingface dataset:
Preexposure Prophylaxis for HIV Prevention in the United States: An Overview and Update
Authors: Dhir Amit “Mickey”
Published: November 2023

There were 36,136 new HIV diagnoses in the United States and dependent areas in 2021, despite a 12% reduction in estimated HIV incidence from 2017 to 2021. The burden of HIV remains disproportionately high among certain populations, including gay and bisexual men, Black/African American individuals, and Hispanic/Latino individuals, and racial and ethnic health care disparities persist. The Ending the HIV Epidemic initiative aims to significantly reduce new infections, with a focus on HIV prevention, particularly the use of preexposure prophylaxis (PrEP). However, challenges remain in achieving equitable PrEP distribution. As frontline health care providers, nurses play a pivotal role in this battle against HIV. This article provides an update on PrEP screening recommendations, the types of PrEP available, dosing, adverse effects, and the role of nurses in patient support and monitoring.
A Nurse-Led Implementation Science Specialist Program
Authors: Russell-Babin Kathleen , Friesen Mary Ann , O'Brien Anne-Marie , McLaughlin Maureen Kirkpatrick , Messing Jonathan , Mowery Bernice , Bettencourt Amanda P. , Graling Paula R.
Published: November 2023

A well-known challenge in health care is integrating evidence into practice. Implementation science (IS) is a growing field that promotes the sustainable application of evidence-based practice (EBP) to clinical care. Health care organizations have an opportunity to support sustainable change by creating robust IS infrastructures that engage nurses in the clinical environment. Integrating IS into a nursing shared governance model is an ideal vehicle to empower direct care nurses to sustain EBP. Importantly, an IS infrastructure may also promote nurse retention and increase interdisciplinary collaboration. This article, the first in a series on applying IS, describes how a multisite health care organization developed a systemwide nurse-led IS Specialist program within a shared governance model.
General anesthesia is an independent predictor for worse maternal outcome in pregnant pulmonary arterial hypertension patients without cardiac shunt but not for those with shunt
Authors: Lu Weida , Li Min , Ji Fuqing , Feng Hua , Qie Liangyi , Li Guo , Ji Qiushang , Ling Mingying , Jiang Fan , Cui Xiaopei
Published: November 2023

Background

Although pregnancy imposes extra risk in patients with pulmonary arterial hypertension (PAH), hemodynamic characteristics vary between PAH patients with and without cardiac shunts. However, previous studies did not take hemodynamic differences in PAH patients into consideration for pregnancy outcome analysis. We aimed to identify predictors for peripartum outcome of PAH patients without/with cardiac shunt.

Methods

We retrospectively analyzed the medical records of PAH gravidae parturiated by cesarean delivery (C-section) from 4 hospitals. Maternal death and major adverse cardiac events (MACEs) occurring during pregnancy or within 6 weeks postpartum were defined as composite end points. Risk factors for end points were analyzed separately in patients with and without cardiac shunt. The effect of general anesthesia on MACEs and maternal death was analyzed by Mantel-Haenszel hierarchical analysis considering cardiac shunts.

Results

One hundred eighty-one PAH gravidae were included, of whom 85 had PAH without cardiac shunt and 96 with shunt. Patients who met combined end points were 19/85 in those without shunt compared with 23/96 in those with shunt. The mortality rates were 11.8% and 9.4%, respectively. Both World Health Organization functional class (WHO-FC) III/IV and general anesthesia were predictors for gravidae without shunt, whereas only WHO-FC III/IV was a predictor for gravidae with shunt. General anesthesia increased the MACE risk (odds ratio, 9.000; 95% confidence interval, 2.628–30.820) and maternal mortality (odds ratio, 11.000; 95% confidence interval, 2.595–46.622; P = 0.039) in patients without cardiac shunt but not in those with shunt during C-section.

Conclusion

All PAH gravidae with WHO-FC III/IV are at high risk and should receive intensive care. General anesthesia should be avoided during C-section for PAH gravidae without a cardiac shunt.
Prevalence, Clinical Characteristics and Risk Factors of Post-COVID-19 Condition in a Multicenter Pediatric Primary and Hospital Care Cohort
Authors: Gatell Anna , López Núria , Balaguer-Martínez Josep , González Xoan , Martín Ramona , Quezada Gabriela , Lobato Zulema , Ruiz Montserrat , Vilà Mònica , Burgaya Silvia , Sánchez Almudena , Giribet Mercè , Biosca Mireia , Canadell Dolors , Alcover Elena , Soriano-Arandes Antoni
Published: November 2023

The prevalence of post-COVID-19 condition is not well defined. We describe a cohort of 244 children diagnosed with COVID-19 and followed up for 6 months, in which 4.9% of patients had persistent symptoms at 12 weeks. Anosmia was the most frequent symptom. Being female and having more than 3 symptoms in acute infection were associated with an increased risk of post-COVID.
Corneal endothelial safety profile in minimally invasive glaucoma surgery
Authors: Ahmed Iqbal Ike K. , Sheybani Arsham , De Francesco Ticiana , Samuelson Thomas W.
Published: November 2023

Purpose:

To compare 5-year corneal endothelial safety of 3 minimally invasive glaucoma surgery (MIGS) devices (iStent inject, Hydrus Microstent, CyPass Micro-Stent).

Setting:

U.S. multicenter trials.

Design:

Post hoc 5-year analysis from prospective randomized single-masked pivotal trials.

Methods:

Mild to moderate open-angle glaucoma subjects received a MIGS implant with phacoemulsification (implant + phaco) or phaco alone (control). In addition, 5-year end points comparing the implant and control groups included proportion of eyes with significant endothelial cell loss (ECL) (>30% or ≥30% vs baseline) and mean endothelial cell density (ECD).

Results:

Comparable proportions of eyes in the iStent inject + phaco and control groups had significant 60-month ECL (9.4% vs 6.3%, respectively, diff: 3.2%, 95% CI, −5.0% to 11.3%, P = .77). Hydrus (20.8% vs 10.6%, diff: 10.2%, 95% CI, 3.2% to 17.2%, P = .01) and CyPass (27.2% vs 10.0%, diff: 17.2%, 95% CI, 5.6% to 28.7%, P = .02) had more eyes with ECL vs controls (iStent inject 1.49X, Hydrus 1.96X, CyPass 2.72X vs controls). Mean ECD over 60 months for iStent inject was indistinguishable vs control, whereas greater ECL was observed primarily 3 months postoperative (Hydrus) or accelerated after 2 years (CyPass). No iStent inject or Hydrus subjects developed persistent corneal edema, whereas 7 CyPass-implanted eyes developed ECL-related complications.

Conclusions:

Through 5 years postoperative, there were no differences in proportion of eyes with significant ECL or mean ECD between the iStent inject and control groups. There was greater 5-year ECL and lower ECD in the Hydrus and CyPass groups vs controls. The Hydrus ECL rate mirrored control after 3 months; the CyPass ECL rate accelerated vs control.
THE THERAPEUTIC EFFICACY OF PLASMAPHERESIS FOR SEPSIS WITH MULTIPLE ORGAN FAILURE: A PROPENSITY SCORE–MATCHED ANALYSIS BASED ON THE MIMIC-IV DATABASE
Authors: Yan Danyang , Yao Run , Xie Xi , Fu Xiangjie , Pei Siya , Wang Yanjie , Xu Daomiao , Li Ning
Published: November 2023

Background: Despite advancements in sepsis treatment, mortality remains high. Plasmapheresis (PE) targeting multiple pathways simultaneously seems to be a potential treatment option, but evidence is insufficient. We aimed to investigate the efficacy of PE for sepsis with multiple organ failure (MOF). Method: Septic patients with MOF were identified from the Medical Information Mart for Intensive Care IV database. Patients who received PE were matched with those receiving conventional therapy via propensity score matching. Regression analyses evaluated the association between PE and outcomes. The Kaplan-Meier (KM) method was used to analyze the survival probability. The generalized additive mixed model investigated early indexes changes’ association with treatment modalities and 28-day mortality. Results: Nine hundred six septic patients with MOF were enrolled. After propensity score matching, PE and conventional groups consisted of 60 cases each. Plasmapheresis was associated with a reduced risk of 28-day mortality (hazard ratio [HR], 0.50; 95% confidence interval [CI], 0.27–0.94), 1-year mortality (HR, 0.44; 95% CI, 0.26–0.74), and in-hospital mortality (HR, 0.38; 95% CI, 0.20–0.71). The KM curves demonstrated significant differences in survival probability between groups. Compared with the conventional group, the sequential organ failure assessment, norepinephrine dosage, prothrombin time, actate dehydrogenase, total bilirubin, white blood cells, and immature granulocytes in the PE group significantly decreased over time, while platelets, red blood cells, and hemoglobin significantly increased over time. Conclusions: Plasmapheresis demonstrated an association with reduced risks of 28-day, in-hospital and 1-year mortality in septic patients with MOF. Moreover, plasmapheresis might exhibit the potential to improve outcomes by improving organ function, hemodynamics, and restoring several indicators, such as coagulation, anemia, and inflammation.
A murky ruling threatens the fate of millions of US wetlands
Authors: Simmons B. Alexander , Beck Marcus W. , Flaherty-Walia Kerry , Lewis Jessica , Sherwood Ed
Published: November 2023

For decades, federal protections were extended to wetlands adjacent to navigable “waters of the US” by the Clean Water Act. In itsSackett v. EPAruling, however, the US Supreme Court redefined the meaning of “adjacent,” eliminating protections to wetlands without a continuous surface connection to these waters (i.e., geographically isolated wetlands). Yet it remains unclear how this continuous surface test will work in reality, where ecological connectivity often extends beyond physical connectivity. Here, we estimate that 22-36% of US wetlands could be considered geographically isolated, depending upon how isolation is defined on the ground, with wetlands in the Midwest and Northeast at greatest risk of losing protection. Stable state-level protections are urgently needed to secure the country’s wetlands from further pollution and destruction.

One-Sentence Summary

Over 3 million wetlands could be considered “geographically isolated” and lose extended protections from the Clean Water Act.
Testing-isolation interventions will likely be insufficient to contain future novel disease outbreaks
Authors: Demers Jeffery , Fagan William F. , Potluri Sriya , Calabrese Justin M.
Published: November 2023

When novel human diseases emerge into naive populations, identification and isolation of infected individuals forms the first line of defense against the invading pathogens1,2. Diagnostic testing plays a critical role3,4, but health agencies unprepared for a novel disease invasion may struggle to meet the massive testing capacities demanded by an epidemic outbreak5, potentially resulting in a failure of epidemic containment as with COVID-196. What factors make a disease controllable versus uncontrollable with limited testing supplies remains unclear. Specifically, is the failure of testing-isolation unique to COVID-19, or is this a likely outcome across the spectrum of disease traits that may constitute future epidemics? Here, using a generalized mathematical disease model parameterized for each of seven different human diseases, we show that testing-isolation strategies will typically fail to contain epidemic outbreaks at practicably achievable testing capacities. From this analysis, we identify three key disease characteristics that govern controllability under resource constraints; the basic reproduction number, mean latent period, and non-symptomatic transmission index. Interactions among these characteristics play prominent roles in both explaining controllability differences among diseases and enhancing the efficacy of testing-isolation in combination with transmission-reduction measures. This study provides broad guidelines for managing controllability expectations during future novel disease invasions, describing which classes of diseases are most amenable to testing-isolation strategies alone and which will necessitate additional transmission-reduction measures like social distancing.
Structural analysis of the Sterile alpha motif (SAM) domain of the Arabidopsis mitochondrial tRNA import receptor
Authors: Olasz Bence , Smithers Luke , Evans Genevieve L. , Anandan Anandhi , Murcha Monika W. , Vrielink Alice
Published: November 2023

Mitochondria are membrane bound organelles of endosymbiotic origin with limited protein coding capacity. As a consequence, the continual import of nuclear-encoded protein and nucleic acids such as DNA and small non-coding RNA is required and essential for maintaining organelle mass, number and activity. As plant mitochondria do not encode all the necessary tRNA types required, the import of cytosolic tRNA is vital for organelle maintenance. Recently, two mitochondrial outer membrane proteins, named Tric1 and Tric2, for tRNA import component, were shown to be involved in the import of cytosolic tRNA. Tric1/2 binds tRNAalavia conserved residues in the C-terminal Sterile Alpha Motif (SAM) domain. Here we report the X-ray crystal structure of the Tric1 SAM domain. We identified the ability of the SAM domain to form a helical superstructure with 6 SAM domains per helical turn and key amino acid residues responsible for its formation. We determined that the oligomerization of Tric1 SAM domain was essential for protein function whereby mutation of Gly241 resulted in the disruption of the oligomer and the loss of RNA binding capability in Tric1. Furthermore, complementation ofArabidopsis thalianaTric1/2 knockout lines with a mutated Tric1 failed to restore the defective plant phenotype suggesting the oligomerization is essential for functionin planta. AlphaFold2 structure prediction of the SAM domain and Tric1 support a cyclic hexamer generating a pore of sufficient dimensions to transfer tRNA across the mitochondrial membrane. Our results highlight the importance of oligomerization of Tric1 for protein function.
Estimation of the instantaneous spike train variability
Authors: Rajdl K. , Kostal L.
Published: November 2023

The variability of neuronal spike trains is usually measured by the Fano factor or the co-efficient of variation of interspike intervals, but their estimation is problematic, especially with limited amount of data. In this paper we show that it is in fact possible to estimate a quantity equivalent to the Fano factor and the squared coefficient of variation based on the intervals from only one specific (random) time. This leads to two very simple but precise Fano factor estimators, that can be interpreted as estimators of instantaneous variability. We derive their properties, evaluate their accuracy in various situations and show that they are often more accurate than the standard estimators. The presented estimators are particularly suitable for the case where variability changes rapidly.
Mitonuclear interactions impact aerobic metabolism in hybrids and may explain mitonuclear discordance in young, naturally hybridizing bird lineages
Authors: McDiarmid Callum S. , Hooper Daniel M. , Stier Antoine , Griffith Simon C.
Published: November 2023

Understanding genetic incompatibilities and genetic introgression between incipient species are major goals in evolutionary biology. Mitochondrial genes evolve rapidly and exist in dense gene networks with coevolved nuclear genes, suggesting that mitochondrial respiration may be particularly susceptible to disruption in hybrid organisms. Mitonuclear interactions have been demonstrated to contribute to hybrid disfunction between deeply divergent taxa crossed in the laboratory, but there are few empirical examples of mitonuclear interactions between younger lineages that naturally hybridise. Here we use experimental crosses and high resolution respirometry to provide the first evidence in a bird that inter-lineage mitonuclear interactions impact mitochondrial aerobic metabolism. Specifically, respiration capacity of the two paternal backcrosses (with mismatched mito-nuclear combinations) differ from one another, although they do not differ to the parental groups or maternal backcrosses as we would expect of mitonuclear disruptions. In the wild hybrid zone between these subspecies the mitochondrial cline centre is shifted west of the nuclear cline centre, which is consistent with the direction of our experimental results. Our results therefore demonstrate asymmetric mitonuclear interactions that impact the capacity of cellular mitochondrial respiration and may help to explain the geographic discordance between mitochondrial and nuclear genomes observed in the wild.
Chlamydiae in cnidarians: Shared functional potential despite broad taxonomic diversity
Authors: Maire Justin , Collingro Astrid , Horn Matthias , van Oppen Madeleine J. H.
Published: November 2023

Cnidarians, such as corals and sea anemones, associate with a wide range of bacteria that have essential functions, including nutrient cycling and the production of antimicrobial compounds. Within cnidarians, bacteria can colonize all microhabitats including the tissues. Among them are obligate intracellular bacteria of the phylum Chlamydiota (chlamydiae) whose impact on cnidarian hosts and holobionts remain unknown. Here, we conducted a meta-analysis of previously published cnidarian 16S rRNA gene metabarcoding data and eight metagenome-assembled genomes (MAGs) of cnidarian-associated chlamydiae to decipher their diversity and functional potential. While the metabarcoding dataset showed an enormous diversity of cnidarian-associated chlamydiae, five out of eight MAGs were affiliated with the Simkaniaceae family. The other three MAGs were assigned to the Parasimkaniaceae, Rhabdochlamydiaceae, and Anoxychlamydiaceae, respectively. All MAGs were associated with corals and showed a functional potential insufficient for an independent existence, lacking any nucleotide or vitamin and most amino acid biosynthesis pathways. Hallmark chlamydial genes, such as a type III secretion system, nucleotide transporters, and genes for host interaction, were encoded in all MAGs. Together these observations suggest an obligate intracellular lifestyle of cnidarian-associated chlamydiae. Cnidarian-associated chlamydiae lacked unique genes, suggesting the core chlamydial genetic arsenal may be flexible enough to infect many eukaryotic hosts, including cnidarians. Additional studies are needed to understand how chlamydiae interact with their cnidarian host, and other microbes in cnidarian holobionts. This first study of the diversity and functional potential of cnidarian-associated chlamydiae improves our understanding of both the cnidarian microbiome and the chlamydial lifestyle and host range.
Diverse Configurations of Erroneous Predictive Coding Across Brain Hierarchies in a Non-Human Primate Model of Autism Spectrum Disorder
Authors: Chao Zenas C. , Komatsu Misako , Matsumoto Madoka , Iijima Kazuki , Nakagaki Keiko , Ichinohe Noritaka
Published: November 2023

In autism spectrum disorder (ASD), atypical sensory experiences are often associated with irregularities in predictive coding, which proposes that the brain creates hierarchical sensory models via a bidirectional process of predictions and prediction errors. However, it remains unclear how these irregularities manifest across different functional hierarchies in the brain. To address this, we used high-density electrocorticography (ECoG) in a non-human primate model of ASD during an auditory task with two layers of temporal control, and applied a quantitative model to quantify the integrity of predictive coding across two distinct hierarchies. Our results demonstrate that ASD is characterized by sensory hypersensitivity and unstable predictions across two brain hierarchies, and reveal the associated spatio-spectro-temporal neural signatures. Importantly, we observe diverse configurations of underestimation or overestimation of sensory regularities within these hierarchies. This work provides a multi-layered biomarker for ASD, contributing to our understanding of its diverse symptoms.
Rhizonet: Image Segmentation for Plant Root in Hydroponic Ecosystem
Authors: Ushizima Daniela , Sordo Zineb , Andeer Peter , Sethian James , Northen Trent
Published: November 2023

Digital cameras have the ability to capture daily images of plant roots, allowing for the estimation of root biomass. However, the complexities of root structures and noisy image backgrounds pose challenges for advanced phenotyping. Manual segmentation methods are laborious and prone to errors, which hinders experiments involving several plants. This paper introduces Rhizonet, a supervised deep learning approach for semantic segmentation of plant root images. Rhizonet harnesses a Residual U-Net backbone to enhance prediction accuracy, incorporating a convex hull operation to precisely outline the largest connected component. The primary objective is to accurately segment the biomass of the roots and analyze their growth over time. The input data comprises color images of various plant samples within a hydroponic environment known as EcoFAB, subject to specific nutrition treatments. Validation tests demonstrate the robust generalization of the model across experiments. This research pioneers advances in root segmentation and phenotype analysis by standardizing processes and facilitating the analysis of thousands of images while reducing subjectivity. The proposed root segmentation algorithms contribute significantly to the precise assessment of the dynamics of root growth under diverse plant conditions.
A novel thin plate spline methodology to model tissue surfaces and quantify tumor cell invasion in organ-on-chip models
Authors: Elton Elizabeth , Strelez Carly , Ung Nolan , Perez Rachel , Ghaffarian Kimya , Matasci Naim , Mumenthaler Shannon M.
Published: November 2023

Organ-on-chip (OOC) models can be useful tools for cancer drug discovery. Advances in OOC technology have led to the development of more complex assays, yet analysis of these systems does not always account for these advancements, resulting in technical challenges. A challenging task in the analysis of these two-channel microfluidic models is to define the boundary between the channels so objects moving within and between channels can be quantified. We propose a novel imaging-based application of a thin plate spline method – a generalized cubic spline that can be used to model coordinate transformations – to model a tissue boundary and define compartments for quantification of invaded objects, representing the early steps in cancer metastasis. To evaluate its performance, we applied our analytical approach to an adapted OOC developed by Emulate, Inc., utilizing a two-channel system with endothelial cells in the bottom channel and colorectal cancer (CRC) patient-derived organoids (PDOs) in the top channel. Initial application and visualization of this method revealed boundary variations due to microscope stage tilt and ridge and valley-like contours in the endothelial tissue surface. The method was functionalized into a reproducible analytical process and web tool – the Chip Invasion and Contour Analysis (ChICA) – to model the endothelial surface and quantify invading tumor cells across multiple chips. To illustrate applicability of the analytical method, we applied the tool to CRC organoid-chips seeded with two different endothelial cell types and measured distinct variations in endothelial surfaces and tumor cell invasion dynamics. Since ChICA utilizes only positional data output from imaging software, the method is applicable to and agnostic of the imaging tool and image analysis system used. The novel thin plate spline method developed in ChICA can account for variation introduced in OOC manufacturing or during the experimental workflow, can quickly and accurately measure tumor cell invasion, and can be used to explore biological mechanisms in drug discovery.
Anticipation of sexually arousing visual event leads to overestimation of elapsed time
Authors: Harjunen Ville Johannes , Spapé Michiel , Ravaja Niklas
Published: November 2023

Subjective estimates of duration are affected by emotional expectations about the future. For example, temporal intervals preceding a threatening event such as an electric shock are estimated as longer than intervals preceding a non-threatening event. However, it has not been unequivocally shown that such temporal overestimation occurs also when anticipating a similarly arousing but appealing event. In this study, we examined how anticipation of visual erotic material influenced perceived duration. Participants did a temporal bisection task, where they estimated durations of visual cues relative to previously learned short and long standard durations. The colour of the to-be-timed visual cue signalled either a chance of seeing a preferred erotic picture at the end of the interval or certainty of seeing a neutral grey bar instead. The results showed that anticipating an appealing event increased the likelihood of estimating the cue duration as long as compared to the anticipation of a grey bar. Further analyses showed that this temporal overestimation effect was stronger for those who rated the anticipated erotic pictures as more sexually arousing. The results thus indicate that anticipation of appealing events has a similar dilating effect on perceived duration as does the anticipation of aversive events.
The Expression of HIV-1 Tat inLactococcus lactis
Authors: Selvam Deepak , D’silva Anish , Gohil Yuvraj , singh Jayendra , Panchapakesan Arun , Hanna Luke Elizabeth , Ranga Udaykumar
Published: November 2023

Efficient expression of functional proteins in heterologous hosts has become the pivotal focus of modern biotechnology and biomedical research. To this end, multiple alternatives toE. coliare being explored for recombinant protein expression.L. lactis, being a gram-positive organism, circumvents the need for an endotoxin removal step during protein purification. We report here the optimisation of the expression of HIV-1 Tat, a notoriously difficult protein, inLactococcus lactissystem. We evaluated five different promoters in two differentLactococcus lactisstrains and examined the effect of pH, glucose, and induction time on the yield and purity of Tat. Finally, the recombinant Tat was functionally competent in transactivating the HIV-1 promoter in HLM-1 reporter cells. Our work provides a scaffold for future work on the expression of toxic proteins inLactococcus lactis.
High-resolution structure of a replication-initiation like configuration of influenza polymerase active site visualises the essential role of a conserved dibasic motif in the PA subunit
Authors: Drncova Petra , Krischuns Tim , Naffakh Nadia , Cusack Stephen
Published: November 2023

Influenza polymerase, comprising subunits PA, PB1 and PB2, transcribes the negative-sense genomic viral RNA (vRNA) into mRNA or replicates it first into complementary RNA (cRNA) and then back to vRNA. Here we investigate the mechanism ofde novo(unprimed) initiation of vRNA to cRNA replication. We present a high-resolution structure of A/little-yellow-shouldered-bat/H17N10 polymerase with the 3’ end of the template in the RNA synthesis active site, both in the apo-state and after soaking with GTP and CTP. The priming GTP and incoming CTP are observed to base-pair to template nucleotides C2 and G3 at the -1 and +1 positions respectively, thus representing a replication initiation-like state. This configuration is stabilised by partial stacking of the tip of the priming loop on the GTP:C2 base-pair and the interaction of PB1/H649 and dibasic motif residues PA/R658 and K659 with the triphosphate of the priming GTP. The dibasic motif is universally conserved in orthomyxovirus PA subunits. Trans-complementation assays in cells using mutants of PA/K659 show that the dibasic motif is specifically essential for replication. These results shed light on the mechanism of replication initiation even though vRNA to cRNA replication is expected to be terminally initiated, with priming ATP and incoming GTP base-pairing to template nucleotides U1 and C2 at the -1 and +1 positions respectively, implying a different position of the template.
The staphylococcal type VII secretion system impacts daptomycin sensitivity through controlling bacterial cell envelope integrity
Authors: Smith Victoria , Chandrasekharan Giridhar , Watkins Kate E. , Marset Ramon Garcia , Yap Jeannifer , Perrier Sebastien , Tchoupa Arnaud Kengmo , Unnikrishnan Meera
Published: November 2023

TheStaphylococcus aureustype VII secretion system (T7SS) plays an important role in bacterial virulence during infection. However, T7SS functions during infection and in bacterial physiology are poorly understood. Here, we demonstrate thatS. aureusstrains lacking the T7SS transporter EssC or effectors, EsxC and EsxA, were highly sensitive to the important last resort drug, daptomycin. T7SS mutants displayed decreased membrane fluidity, altered cell membrane protein localisation, distinct cell surface morphologies, with effects on cell wall synthesis as well as surface charge under normal growth conditions, indicating that the T7SS is critical to cell envelope function. Daptomycin binding was enhanced in the mutants, whose membranes were more permeable when treated with the drug. Furthermore, the lack of EsxC enhanced daptomycin sensitivity during intracellular infection and during murine skin infection. Thus, our data show that the staphylococcal T7SS impacts sensitivity to membrane-acting drugs through modulating membrane integrity, indicating its potential as a drug target.
CEP44 is required for maintaining centriole duplication and spindle integrity
Authors: Zhang Donghui , Wei Wenlu , Zou Xiaopeng , Meng Hui , Li Fangyuan , Yao Minjun , Teng Junling , Huang Ning , Chen Jianguo
Published: November 2023

In animal cells, the centrosome, consisting of two centrioles, duplicates only once per cell cycle for bipolar spindle formation. Defective centriole duplication results in abnormal spindle formation and chromosome missegregation, which is closely linked to tumor growth. However, the molecular mechanisms licensing only one centriole duplication cycle within a cell cycle are less well known. Here we found that CEP44 is negatively correlated with breast carcinoma. CEP44, jointly with CEP57 and CEP57L1, maintains centriole engagement in the interphase to ensure centriole duplication once per cell cycle. Depletion of CEP44 leads to centriole overduplication because of premature centriole disengagement, and multipolar spindle formation. Additionally, CEP44 is phosphorylated by Aurora A at the G2/M phase to facilitate spindle localization and maintain spindle integrity. Collectively, our results show the function of CEP44 in spindle formation by preventing centriole overduplication and maintaining spindle integrity, and CEP44 may serve as a potential marker for breast carcinoma prognosis.
Metagenome profiling and containment estimation through abundance-corrected k-mer sketching with sylph
Authors: Shaw Jim , Yu Yun William
Published: November 2023

Profiling metagenomes against databases allows for the detection and quantification of mi-crobes, even at low abundances where assembly is not possible. We introduce sylph (https://github.com/bluenote-1577/sylph), a metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. Sylph is the most accurate method on the CAMI2 marine dataset, and compared to Kraken2 for multi-sample profiling, sylph takes 10× less CPU time and uses 30× less memory. Sylph’s ANI estimates provide an orthogonal signal to abundance, enabling an ANI-based metagenome-wide association study for Parkinson’s disease (PD) against 289,232 genomes while confirming known butyrate-PD associations at the strain level. Sylph takes < 1 minute and 16 GB of RAM to profile against 85,205 prokaryotic and 2,917,521 viral genomes, detecting 30× more viral sequences in the human gut compared to RefSeq. Sylph offers precise, efficient profiling with accurate containment ANI estimation for even low-coverage genomes.
YeastIT: Reducing mutational bias for in vivo directed evolution using a novel yeast mutator strain based on dual adenine-/cytosine-targeting and error-prone DNA repair
Authors: Napiorkowska Marta , Fischer Katrin , Penner Matthew , Knyphausen Philipp , Hollfelder F.
Published: November 2023

Engineering proteins with new functions and properties often requires navigating large sequence spaces through rounds of iterative improvement. However, a disparity exists between the gradual pace of natural long-term evolution and a typical laboratory evolution workflow that relies on enriching functional variants from highly diverse in vitro generated libraries through very few screening rounds. Laboratory experiments often eschew presumed natural strategies such as neutral/non-adaptive and multi-phase evolution trajectories, and therefore mutagenesis technologies suitable for long ‘nature-like’ timescales are needed. Here, we introduce YeastIT, a novel in vivo mutagenesis tool for protein engineering that leverages anS. cerevisiaestrain engineered to exhibit mutagenic activity directed to the gene of interest, allowing its continuous diversification. Mutagenesis is achieved by generating DNA damage through nucleoside deamination, followed by introduction of mutations by harnessing the process of error-prone DNA translesion synthesis. By eliminating the transformation step, YeastIT allows multiple rounds of screening or selection without interruptions for library diversification, thereby enabling long-term and continuous evolution campaigns. Our characterization of the mutational spectrum and frequency of the YeastIT-generated libraries, and its comparison to other methods (error-prone PCR, PACE, MutaT7, eMutaT7, OrthoRep, TRIDENT, EvolVR) demonstrates comparable mutation rates combined with a significant reduction in mutagenic bias relative to most of the alternatives. To validate YeastIT, we carried out directed evolution of a DARPin binding protein to achieve a 15-fold improved affinity. YeastIT thus provides a tool for exploring different evolutionary trajectories which overcomes previous limitations of variant availability (due to bias and low mutation rates) and emulates the way proteins emerge in Nature.
A novel highly divergent enteric calicivirus in a bovine calf, India
Authors: Kumar Naveen , Kaushik Rahul , Yadav Pragya , Sircar Shubhankar , Shete-Aich Anita , Singh Ashutosh , Malik Yashpal Singh
Published: November 2023

In 2015, a novel highly divergent bovine calicivirus was detected in an Indian calf with enteritis. Phylogenetic analysis linked it to theNeboviruswith only 38.5% sequence identities, emphasizing the need for separate taxonomic classification. Furthermore, PCR screening detected these unique caliciviruses widely in India’s northern states.
Designer antisense circRNAGFPreduces GFP protein abundance in transgenic Arabidopsis protoplasts in a sequence-specific manner, independent of RNAi pathways
Authors: Hossain M , Pfafenrot C , Imani J , Šečić E , Sede A , Galli M , Heinlein M , Bindereif A , Ladera-Carmona M , Kogel KH
Published: November 2023

Circular RNAs (circRNAs) are single-stranded molecules that have attracted increasing attention in recent years due to their covalently closed structure and their diverse functional roles in mammalian cells, where they are involved in the regulation of gene expression and protein function. Increasing evidence suggests that circRNAs have similar functions in plants, where they play a role in plant development, resistance to biotic stress, and abiotic stress tolerance. Here, we investigated the agronomically relevant question of whether synthetic designer circRNAs can be used to modulate in a sequence-specific manner gene expression in plants. We show that treatment ofGFP-expressing Arabidopsis protoplasts with designer 50 nt GFP antisense circRNA (circRNAGFP) reduces the cellular accumulation of the reporter protein in a sequence-specific and dose-dependent manner. This inhibitory activity of circRNAGFPwas not abolished in various Arabidopsisagoanddclmutants with defective RNAi pathways. Moreover, and in contrast to other types of RNA such as double-stranded (ds)RNA, circRNAs did not induce a PTI response in plant leaves. We discuss the possibility that circRNA may be applied to regulate endogenous plant genes and thus may have future potential as a novel bioherbicide.
SmCCNet 2.0: A Comprehensive Tool for Multi-omics Network Inference with Shiny Visualization
Authors: Liu Weixuan , Vu Thao , Konigsberg Iain , Pratte Katherine , Zhuang Yonghua , Kechris Katerina
Published: November 2023

Sparse multiple canonical correlation network analysis (SmCCNet) is a machine learning technique for integrating omics data along with a variable of interest (e.g., phenotype of complex disease), and reconstructing multi-omics networks that are specific to this variable. We present the second-generation SmCCNet (SmCCNet 2.0) that adeptly integrates single or multiple omics data types along with a quantitative or binary phenotype of interest. In addition, this new package offers a streamlined setup process that can be configured manually or automatically, ensuring a flexible and user-friendly experience.

Availability

This package is available in both CRAN:https://cran.r-project.org/web/packages/SmCCNet/index.htmland Github:https://github.com/KechrisLab/SmCCNetunder the MIT license. The network visualization tool is available athttps://smccnet.shinyapps.io/smccnetnetwork/.
Molecular regulation of retinal regeneration is context specific
Authors: Emmerich Kevin , Hageter John , Hoang Thanh , Lyu Pin , Sharrock Abigail V. , Ceisel Anneliese , Thierer James , Chunawala Zeeshaan , Nimmagadda Saumya , Palazzo Isabella , Matthews Frazer , Zhang Liyun , White David T. , Rodriquez Catalina , Graziano Gianna , Marcos Patrick , May Adam , Mulligan Tim , Reibman Barak , Saxena Meera T. , Ackerley David F. , Qian Jiang , Blackshaw Seth , Horstick Eric , Mumm Jeff S.
Published: November 2023

Many genes are known to regulate retinal regeneration following widespread tissue damage. Conversely, genes controlling regeneration following limited retinal cell loss, akin to disease conditions, are undefined. Combining a novel retinal ganglion cell (RGC) ablation-based glaucoma model, single cell omics, and rapid CRISPR/Cas9-based knockout methods to screen 100 genes, we identified 18 effectors of RGC regeneration kinetics. Surprisingly, 32 of 33 previously known/implicated regulators of retinal tissue regeneration were not required for RGC replacement; 7 knockouts accelerated regeneration, includingsox2, olig2,andascl1a. Mechanistic analyses revealed loss ofascl1aincreased “fate bias”, the propensity of progenitors to produce RGCs. These data demonstrate plasticity and context-specificity in how genes function to control regeneration, insights that could help to advance disease-tailored therapeutics for replacing lost retinal cells.

One sentence summary

We discovered eighteen genes that regulate the regeneration of retinal ganglion cells in zebrafish.
Behavioral and neuropathological features of Alzheimer’s disease are attenuated in 5xFAD mice treated with intranasal GHK peptide
Authors: Tucker Matthew , Liao Gerald Yu , Park Joo Young , Rosenfeld Manuela , Wezeman Jackson , Mangalindan Ruby , Ratner Dan , Darvas Martin , Ladiges Warren
Published: November 2023

Efforts to find disease modifying treatments for Alzheimer’s disease (AD) have met with limited success in part because the focus has been on testing drugs that target a specific pathogenic mechanism. Multiple pathways have been implicated in the pathogenesis of AD. Hence, the probability of more effective treatment for AD is likely increased by using an intervention that targets more than one pathway. The naturally occurring peptide GHK (glycyl-L-histidyl-L-lysine), as a GHK-Cu complex, supports angiogenesis, remodeling, and tissue repair, has anti-inflammatory and antioxidant properties, and has been shown to improve cognitive performance in aging mice. In order to test GHK-Cu as a neurotherapeutic for AD, male and female 5xFAD transgenic mice on the C57BL/6 background at 4 months of age were given 15 mg/kg GHK-Cu intranasally 3 times per week for 3 months until 7 months of age. Results showed that intranasal GHK-Cu treatment delayed cognitive impairment, reduced amyloid plaques, and lowered inflammation levels in the frontal cortex and hippocampus. These observations suggest additional studies are warranted to investigate the potential of GHK-Cu peptide as a promising treatment for AD.
Alternative substitutions of N332 in HIV-1AD8gp120 differentially affect envelope glycoprotein function and viral sensitivity to broadly neutralizing antibodies targeting the V3-glycan
Authors: Jeffy Jeffy , Parthasarathy Durgadevi , Ahmed Shamim , Cervera-Benet Héctor , Xiong Ulahn , Harris Miranda , Mazurov Dmitriy , Pickthorn Stephanie , Herschhorn Alon
Published: November 2023

The envelope glycoprotein (Env) trimer on the surface of human immunodeficiency virus type I (HIV-1) mediates viral entry into host CD4+ T cells and is the sole target of neutralizing antibodies. Broadly neutralizing antibodies (bnAbs) that target gp120 V3-glycan of HIV-1 Env trimer are potent and block the entry of diverse HIV-1 strains. Most V3-glycan bnAbs interact, to a different extent, with a glycan attached to N332 but Asn at this position is not absolutely conserved or required for HIV-1 entry based on prevalence of N332 in different circulating HIV-1 strains from diverse clades. Here, we studied the effects of amino acid changes at position 332 of HIV-1AD8Envs on HIV-1 sensitivity to antibodies, cold exposure, and soluble CD4. We further investigated how these changes affect Env function and HIV-1 infectivityin vitro. Our results suggest robust tolerability of HIV-1AD8Env N332 to changes with specific changes that resulted in extended exposure of gp120 V3 loop, which is typically concealed in most primary HIV-1 isolates. Viral evolution leading to Asn at position 332 of HIVAD8Envs is supported by the selection advantage of high levels of cell-cell fusion, transmission, and infectivity even though cell surface expression levels are lower than most N332 variants. Thus, tolerance of HIV-1AD8Envs to different amino acids at position 332 provides increased flexibility to respond to changing conditions/environments and to evade the immune system. Modeling studies of the distance between N332 glycan and specific bnAbs was in agreement with N332 glycan dependency on bnAb neutralization. Overall, our studies provide insights into the contribution of specific amino acids at position 332 to Env antigenicity, stability on ice, and conformational states.
vmrseq: probabilistic modeling of single-cell methylation heterogeneity
Authors: Shen Ning , Korthauer Keegan
Published: November 2023

Single-cell DNA methylation measurements reveal genome-scale inter-cellular epigenetic heterogeneity, but extreme sparsity and noise challenges rigorous analysis. Previous methods to detect variably methylated regions (VMRs) have relied on predefined regions or sliding windows, and report regions insensitive to heterogeneity level present in input. We present vmrseq, a statistical method that overcomes these challenges to detect VMRs with increased accuracy in synthetic benchmarks and improved feature selection in case studies. vmrseq also highlights context-dependent correlations between methylation and gene expression, supporting previous findings and facilitating novel hypotheses on epigenetic regulation. vmrseq is available athttps://github.com/nshen7/vmrseq.
Structure of the γ-tubulin ring complex-capped microtubule
Authors: Aher Amol , Urnavicius Linas , Xue Allen , Neselu Kasahun , Kapoor Tarun M.
Published: November 2023

Microtubules are composed of α/β-tubulin dimers positioned head-to-tail to form protofilaments that associate laterally in varying numbers. It is not known how cellular microtubules assemble with the canonical 13-protofilament architecture, resulting in micrometer-scale α/β-tubulin tracks for intracellular transport that align with, rather than spiral along, the filament’s long-axis. We report that the human ∼2.3MDa γ-tubulin ring complex (γ-TuRC), an essential regulator of microtubule formation that contains 14 γ-tubulins, selectively nucleates 13-protofilament microtubules. Cryo-EM reconstructions of γ-TuRC-capped microtubule minus-ends reveal the extensive intra- and inter-domain motions of γ-TuRC subunits that accommodate its actin-containing luminal bridge and establish lateral and longitudinal interactions between γ- and α-tubulins. Our structures reveal how free γ-TuRC, an inefficient nucleation template due to its splayed conformation, transforms into a stable cap that blocks addition or loss of α/β-tubulins from minus-ends and sets the lattice architecture of cellular microtubules.

One Sentence Summary

Structural insights into how the γ-tubulin ring complex nucleates and caps a 13-protofilament microtubule.
XCP-D: A Robust Pipeline for the post-processing of fMRI data
Authors: Mehta Kahini , Salo Taylor , Madison Thomas , Adebimpe Azeez , Bassett Danielle S. , Bertolero Max , Cieslak Matthew , Covitz Sydney , Houghton Audrey , Keller Arielle S. , Luo Audrey , Miranda-Dominguez Oscar , Nelson Steve M. , Shafiei Golia , Shanmugan Sheila , Shinohara Russell T. , Sydnor Valerie J. , Feczko Eric , Fair Damien A. , Satterthwaite Theodore D.
Published: November 2023

Functional neuroimaging is an essential tool for neuroscience research. Pre-processing pipelines produce standardized, minimally pre-processed data to support a range of potential analyses. However, post-processing is not similarly standardized. While several options for post-processing exist, they tend not to support output from disparate pre-processing pipelines, may have limited documentation, and may not follow BIDS best practices. Here we present XCP-D, which presents a solution to these issues. XCP-D is a collaborative effort between PennLINC at the University of Pennsylvania and the DCAN lab at the University at Minnesota. XCP-D uses an open development model on GitHub and incorporates continuous integration testing; it is distributed as a Docker container or Singularity image. XCP-D generates denoised BOLD images and functional derivatives from resting-state data in either NifTI or CIFTI files, following pre-processing with fMRIPrep, HCP, and ABCD-BIDS pipelines. Even prior to its official release, XCP-D has been downloaded >3,000 times from DockerHub. Together, XCP-D facilitates robust, scalable, and reproducible post-processing of fMRI data.