bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of prophylactic prostatectomy as a primary prevention strategy in high-risk germline mutation carriers
Authors: Tiwari Raj , Clark Roderick , Fleshner Neil
Published: July 2022

Purpose of review

Men with high-risk germline mutations are at significantly higher risk of developing and dying from prostate cancer. Current screening and treatment paradigms may lead to missed opportunities for cure. Herein we review the current literature on prevention, screening and treatment of these carriers and explore the potential role of prophylactic prostatectomy in primary prevention of prostate cancer mortality.

Recent findings

Prostate-specific antigen (PSA)-based screening has demonstrated marginal benefits in prostate cancer (PCa) survival and uncertainty remains on its true benefit among high-risk carriers. Recent results indicate that PCa in BRCA 2 carriers occurs at a higher incidence, younger age and progresses more rapidly compared with noncarriers. An intensified screening protocol of MRI and PSA in young carriers demonstrated how using PSA values alone may be insufficient. Current evidence indicates that high-risk carriers have worse survival outcomes after undergoing radical treatment for screening detected disease when compared with noncarriers.

Prophylactic prostatectomy within the context of a clinical trial is a reasonable primary prevention option for discussion with high-risk carriers, especially BRCA2 carriers during the shared decision-making process. Limitations exist in the current strategies of early PSA screening followed by radical treatment in this group.
The past, present, and future of pT0 in bladder cancer clinical trials
Authors: Schober Jared P. , Plimack Elizabeth , Geynisman Daniel M. , Zibelman Matthew
Published: July 2022

Purpose of review

Since the establishment of neoadjuvant chemotherapy as the standard of care for patients with muscle invasive bladder cancer, the pathologic absence of disease, denoted pT0, was found to be predictive of improved overall survival. Accordingly, it has been used in clinical trials as an optimal surrogate outcome measure, even in contemporary nonchemotherapeutic interventions. We review the role of pT0 as a catalyst for change in trial design and its suitability to facilitate more efficient and timely results. In addition, we explore the present and future of cT0, the clinical absence of disease, in defining treatment response and enabling bladder-sparing management options.

Recent findings

The use of pT0 as a surrogate has provided initial results for the efficacy of immunotherapy in the neoadjuvant space. In combination with molecular markers, pT0 has improved our ability to identify treatment responders and its clinical counterpart, cT0, has been integrated into multiple trials to redefine postneoadjuvant chemotherapy management algorithms.

The use of pT0 as a surrogate endpoint in bladder cancer trials has improved clinical trial design, defined efficacy of emerging therapeutics, and has the potential to redefine the postneoadjuvant treatment management for patients seeking bladder-sparing options.
The State of Palliative Care Education in United States Physical Medicine and Rehabilitation Residency Programs: Heterogeneity and Opportunity for Growth
Authors: Tolchin Dorothy W. , Brooks Forrest A. , Knowlton Tiffany
Published: July 2022

Physical medicine and rehabilitation (PM&R) physicians routinely care for patients with serious illness and injury who could benefit from an integrated palliative care approach due to the propensity for high or complex symptom burden. Despite this, it has been unknown whether and how PM&R residency programs are equipping residents with a foundational palliative care skillset. We report national survey results characterizing the current status of palliative care education within United States PM&R residency programs. Programs vary widely in the type and amount of palliative care education provided, with nearly a third of responding programs reporting no palliative care education at all. These findings suggest the need for nationally unifying palliative care education standards for PM&R residency programs to ensure that all PM&R residents have the opportunity to develop a robust palliative lens that can be applied across rehabilitation practice settings. An articulated set of standards could both facilitate achievement of palliative care-specific objectives and support achievement of foundational PM&R residency program objectives.
Pharmaceutical Analysis of Peripherally Inserted Central Catheter Requests Increases the Use of Single-Lumen Catheters: A Prospective Pilot Study
Authors: Chasseigne Virginie , Buisson Marlène , Serrand Chris , Leguelinel-Blache Géraldine , Kinowski Jean-Marie , Goupil Jean , Beregi Jean-Paul , Frandon Julien
Published: July 2022

Objectives

Several studies have suggested a strong relationship between the number of peripherally inserted central catheter (PICC) lumens and the risk of complications. The purpose of this study is to evaluate the impact of the intervention of a clinical pharmacist (CP) on the number of lumens of PICC inserted and assess PICC-related complications.

Method

This prospective monocentric study included all consecutive patients from 5 different units who underwent PICC insertions from September 2017 to March 2018. In the intervention group, the CP validated the pertinence of each PICC request according to the patients’ records, choice of device (single or double lumen), and incompatibilities between treatments. The control group consisted of patients who underwent PICC insertions without a CP intervention. Complications were prospectively recorded up to PICC removal. Multivariate analyses adjusted for sex, age, and PICC line duration were performed.

Results

In the intervention group, 207 PICCs were inserted, 81.2% (n = 168) were single-lumen devices and 18.8% (n = 39) were double-lumen devices. In the control group (n = 77), the use of single-lumen PICCs was significantly lower (n = 48, 62.3%; P = 0.002). After intervention, the overall complication incidence rate decreased from 4.42 to 3.23 per 1000 catheter days (P = 0.082). Considering the overall population, 216 single-lumen PICCs were inserted with significantly fewer complications than double-lumens (respectively n = 16, 16/216 = 7.4%, versus n = 15, 15/68 = 22.1%, P = 0.002). The adjusted odds ratio of double-lumen PICC was 3.83 (95% confidence interval, 1.46–10.07; P = 0.007).

Conclusions

Our study showed the intervention of a CP in the PICC insertion process could increase the use of single-lumen PICCs and tended to reduce associated complications.
The use of mentoring for knowledge translation by allied health: a scoping review
Authors: Howlett Owen , O’Brien Chris , Gardner Marcus , Neilson Cheryl
Published: July 2022

Objective:

To describe how allied health professionals have used mentoring as a knowledge translation strategy to inform practice.

Introduction:

Mentoring has been reported to be used by nursing and medicine as a knowledge translation strategy. It is not known if allied health professionals have also used mentoring to improve their use of research in practice, or what the key mentoring characteristics are that guide its application in allied health settings. Improved understanding of the barriers and facilitators to mentoring in allied health settings may be used to guide the design of future mentoring programs to assist knowledge translation.

Inclusion criteria:

Eligible studies must have included allied health professionals, and used the concept of mentoring to support knowledge translation in the context of healthcare. Primary empirical and synthesized studies were eligible.

Methods:

An a-priori protocol was followed to complete a search of six databases (MEDLINE [OVID], EMBASE [OVID], CINAHL [EBSCO], PsycInfo [OVID], PDQ-Evidence (www.pdq-evidence.org), and Cochrane on the 9 March 2021. Screening for eligibility was conducted by two authors at the title and abstract stage and the full text stage. Selection criteria and the data extraction tool were established prior to the search. Findings are presented in narrative and tabular formats.

Results:

A total of 2053 studies met the inclusion criteria for screening and nine were determined to be eligible for inclusion. Mentoring has been used by allied health professionals to improve the translation of interventional research evidence by clinicians, and to establish clinician skills and knowledge relating to knowledge translation processes. Mentoring was predominantly used as part of a multifaceted knowledge translation strategy alongside educational strategies. Mentoring characteristics such as structure, context, goals, resourcing and dosage varied depending on the context of translation. The specific barriers reported to using mentoring were varied, whereas the facilitators to mentoring were primarily related to the mentor's approach and expertise. The impact of mentoring was primarily measured through the mentee's experience of mentoring.

Conclusions:

Allied health professionals have used mentoring as a knowledge translation strategy to enhance the use of research evidence in their practice and to learn the process of knowledge translation. Mentoring is mostly used in conjunction with other strategies in practice, such as education. The limited number of identified barriers and facilitators to using mentoring as a knowledge translation strategy supports the need for future research to deepen our understanding about the mentoring process.
Asymptotic shape of isolated magnetic domains
Authors: Knüpfer Hans , Stantejsky Dominik
Published: July 2022

We investigate the energy of an isolated magnetized domainΩ⊂Rnforn=2,3. In non-dimensionalized variables, the energy given byE(Ω)=∫Rn|∇χΩ| dx+∫Rn|∇hΩ|2 dxpenalizes the interfacial area of the domain as well as the energy of the corresponding magnetostatic field. Here, the magnetostatic potentialhΩis determined byΔhΩ=∂1χΩ, corresponding to uniform magnetization within the domain. We consider the macroscopic regime|Ω|→∞, in which we derive compactness andΓ-limit which is formulated in terms of the cross-sectional area of the anisotropically rescaled configuration. We then give the solutions for the limit problems.
Life history and the evolutionary loss of parental care
Authors: Udu Isimeme N. , Bonsall Michael B. , Klug Hope
Published: July 2022

Parental care has been gained and lost evolutionarily multiple times. While many studies have focused on the origin of care, few have explored the evolutionary loss of care. Understanding the loss of parental care is important as the conditions that favour its loss will not necessarily be the opposite of those that favour the evolution of care. Evolutionary hysteresis (the case in which evolution depends on the history of a system) could create a situation in which it is relatively challenging to lose care once it has evolved. Here, using a mathematical approach, we explore the evolutionary loss of parental care in relation to basic life-history conditions. Our results suggest that parental care is most likely to be lost when egg and adult death rates are low, eggs mature quickly, and the level of care provided is high. We also predict evolutionary hysteresis with respect to egg maturation rate: as egg maturation rate decreases, it becomes increasingly more costly to lose care than to gain it. This suggests that once care is present, it will be particularly challenging for it to be lost if eggs develop slowly.
Data rescue: saving environmental data from extinction
Authors: Bledsoe Ellen K. , Burant Joseph B. , Higino Gracielle T. , Roche Dominique G. , Binning Sandra A. , Finlay Kerri , Pither Jason , Pollock Laura S. , Sunday Jennifer M. , Srivastava Diane S.
Published: July 2022

Historical and long-term environmental datasets are imperative to understanding how natural systems respond to our changing world. Although immensely valuable, these data are at risk of being lost unless actively curated and archived in data repositories. The practice of data rescue, which we define as identifying, preserving, and sharing valuable data and associated metadata at risk of loss, is an important means of ensuring the long-term viability and accessibility of such datasets. Improvements in policies and best practices around data management will hopefully limit future need for data rescue; these changes, however, do not apply retroactively. While rescuing data is not new, the term lacks formal definition, is often conflated with other terms (i.e. data reuse), and lacks general recommendations. Here, we outline seven key guidelines for effective rescue of historically collected and unmanaged datasets. We discuss prioritization of datasets to rescue, forming effective data rescue teams, preparing the data and associated metadata, and archiving and sharing the rescued materials. In an era of rapid environmental change, the best policy solutions will require evidence from both contemporary and historical sources. It is, therefore, imperative that we identify and preserve valuable, at-risk environmental data before they are lost to science.
Paper wasps form abstract concept of ‘same and different’
Authors: Weise Chloe , Ortiz Christian Cely , Tibbetts Elizabeth A.
Published: July 2022

Concept formation requires animals to learn and use abstract rules that transcend the characteristics of specific stimuli. Abstract concepts are often associated with high levels of cognitive sophistication, so there has been much interest in which species can form and use concepts. A key abstract concept is that of sameness and difference, where stimuli are classified as either
the same as
or
different than
an original stimulus. Here, we used a simultaneous two-item same-different task to test whether paper wasps (
Polistes fuscatus)
can learn and apply a same-different concept. We trained wasps by simultaneously presenting pairs of
same
or
different
stimuli (e.g. colours). Then, we tested whether wasps could apply the concept to new stimuli of the same type (e.g. new colours) and to new stimulus types (e.g. odours). We show that wasps learned a general concept of
sameness
or
difference
and applied it to new samples and types of stimuli. Notably, wasps were able to transfer the learned rules to new stimuli in a different sensory modality. Therefore,
P. fuscatus
can classify stimuli based on their relationships and apply abstract concepts to novel stimulus types. These results indicate that abstract concept learning may be more widespread than previously thought.
Governance Framework and Public Private Partnership for Universal Health Coverage: Findings from India’s Federal Health Structure
Authors: Raman A. Venkat , Lahariya Chandrakant
Published: July 2022

Background

The role of private health sector in advancing universal health coverage is being recognized globally. A number of public private partnership (PPP) strategies have been implemented across the states in India. States (provinces) are primarily responsible for health service delivery in India.

Objectives

To document various PPPs models in health sector across Indian states and to map the policy, legal and institutional eco-system governing such partnerships.

Methods

Desk review followed up with field visits and in-depth interviews. A total of 52 in-depth interviews were conducted from various levels of stakeholders.

Results

Nearly 250 PPP initiatives in health sector across all Indian states were identified and studied. Partnership with the private sector was predominantly in the areas of emergency transport, laboratory diagnosis, and in the delivery of selected primary care services. PPPs in health infrastructure (hospitals and medical colleges) and purchasing arrangements are rapidly emerging across most states. However, only few Indian states have health sector specific PPP policy or legal and/ or institutional framework governing PPPs and organizational units implementing partnership schemes. The capacity to conceive, design, implement, and manage PPPs in health sector was found either absent or insufficient in most states.

Conclusion

Effective partnerships with the private health sector for achieving country’s health goals requires a well enunciated policy and governance framework; detailed assessment of the private health sector market behavior; legal, regulatory, and oversight mechanisms; building organizational structures with capacities, and developing platforms for stakeholder dialogue. Findings from the Indian context could offer useful insights for other low- and middle-income countries aiming to advance towards achieving UHC.
The Lifestyle Factors of Physical Activity and Diet Balance associated with HPV Infection
Authors: Li Yantao , Liu Mengping , Huang Peng , Yang Zhongzhou , Wang Anli
Published: July 2022

Background

Human wellbeing has been linked with lifestyle factors such as physical activity, diet balance, sleep quality, depression, and anxiety. However, few studies illustrate the relationship between such lifestyle factors and HPV infection. In this study, we demonstrate that lifestyle factors might be crucial for reducing the burden of cervical cancer or HPV-related cancer.

Participants and Methods

Participants were recruited through a digital eHealth platform without vaccination from May 2020 to August 2021. Both lifestyle factors and cervicovaginal mucus (CVM) samples to test for HPV outcomes were collected from each participant. In addition, the eHealth platform recorded age and gynecological diseases, which were adjusted to apply for both univariable and multivariable logistic regression. Furthermore, lifestyle factors and HPV serotype were categorized as low, intermediate, and high risk in order to conduct stratification analysis. Finally, lifestyle factors were studied in connection with sole and multiple HPV serotypes.

Results

We recruited 149 HPV positive and 346 HPV negative through HPV detection. Physical activity and diet balance were significantly associated with HPV infection in lifestyle factors (P-values < 0.001) after adjusting for age and gynecological diseases. However, stratified analysis showed three factors were insignificant for HPV infection – namely, sleep quality, depression, and anxiety. Most HPV infections involved a sole HPV serotype (83%), and diet balance was the most significant difference between sole and multiple HPV infections.

Conclusions

Among lifestyle factors, low physical activity or low diet balance can significantly increase HPV infection. In particular, diet balance might be related to the number of HPV serotypes. Our results suggest that exercising and regulating one’s diet may reduce the burden of HPV-related cancer.
Ethnic homophily affects vaccine prioritization strategies
Authors: Kadelka Claus , Islam Md Rafiul , McCombs Audrey , Alston Jake , Morton Noah
Published: July 2022

People are more likely to interact with other people of their ethnicity—a phenomenon known as ethnic homophily. In the United States, people of color are known to hold proportionately more high-contact jobs and are thus more at risk of virus infection. At the same time, these ethnic groups are on average younger than the rest of the population. This gives rise to interesting disease dynamics and non-trivial trade-offs that should be taken into consideration when developing prioritization strategies for future mass vaccine roll-outs.

Here, we study the spread of COVID-19 through the U.S. population, stratified by age, ethnicity, and occupation, using a detailed, previously-developed compartmental disease model. Based on historic data from the U.S. mass COVID-19 vaccine roll-out that began in December 2020, we show, (i) how ethnic homophily affects the choice of optimal vaccine allocation strategy, (ii) that, notwithstanding potential ethical concerns, differentiating by ethnicity in these strategies can improve outcomes (e.g., fewer deaths), and (iii) that the most likely social context in the United States is very different from the standard assumptions made by models which do not account for ethnicity and this difference affects which allocation strategy is optimal.

Highlights

A social mixing model accounting for ethnic homophily and variable job-related risk level is developed.

A scenario that differs strongly from standard homogeneous mixing assumptions best matches U.S. ethnicity-specific death and case counts.

Two trade-offs are explored: Should (i) old or young, and (ii) people of color or White and Asian people first receive COVID-19 vaccines?

Exhaustive simulation of a compartmental disease model identifies the optimal allocation strategy for different demographic groups.

Optimal strategies depend on the underlying mixing pattern and strategies that differentiate vaccine access by ethnicity outperform others.
Integrative analysis of neuroblastoma by single-cell RNA sequencing identifies the NECTIN2-TIGIT axis as a target for immunotherapy
Authors: Wienke Judith , Visser Lindy L. , Kholosy Waleed M. , Keller Kaylee M. , Barisa Marta , Munnings-Tomes Sophie , Carlton Elizabeth , Poon Evon , Rodriguez Ana , Bernardi Ronald , van den Ham Femke , van Hooff Sander R. , Matser Yvette A.H. , Tas Michelle L. , Langenberg Karin P.S. , Lijnzaad Philip , Strijker Josephine G.M. , Sanchez-Bernabeu Alvaro , Cornel Annelisa M. , Holstege Frank C.P. , Gray Juliet , Tytgat Lieve A.M. , de Krijger Ronald R. , Scheijde-Vermeulen Marijn A. , Wijnen Marc H.W.A. , Dierselhuis Miranda , Straathof Karin , Behjati Sam , Wu Wei , Heck Albert J.R. , Koster Jan , Nierkens Stefan , Chesler Louis , Anderson John , Caron Hubert N. , Margaritis Thanasis , van Noesel Max M. , Molenaar Jan J.
Published: July 2022

Pediatric patients with high-risk neuroblastoma have poor survival rates and urgently need more effective treatment options with less side effects. As novel and improved immunotherapies may fill this need, we dissected the immunoregulatory interactions in neuroblastoma by single-cell RNA-sequencing of 25 tumors (10 pre- and 15 post-chemotherapy, including 5 pairs) to identify strategies for optimizing immunotherapy efficacy. Neuroblastomas were infiltrated by NK, T and B cells, and immunosuppressive myeloid populations. NK cells showed reduced cytotoxicity and T cells had a dysfunctional profile. Interaction analysis revealed a vast immunoregulatory network and identified NECTIN2-TIGIT as a crucial immune checkpoint. Combined blockade of TIGIT and PD-L1 significantly reduced neuroblastoma growth, with complete responsesin vivo. Moreover, addition of TIGIT blockade to standard relapse treatment in a chemotherapy-resistantTh-ALKF1174L/MYCN129/SvJ syngeneic model significantly improved survival. Concluding, our integrative analysis of neuroblastoma’s vast immunoregulatory network provides novel targets and a rationale for immunotherapeutic combination strategies.
Plasticity of the proteasome-targeting signal Fat10 enhances substrate degradation
Authors: Negi Hitendra , Ravichandran Aravind , Dasgupta Pritha , Reddy Shridivya , Das Ranabir
Published: July 2022

The proteasome controls levels of most cellular proteins, and its activity is regulated under stress, quiescence, and inflammation. However, factors determining the proteasomal degradation activity remain poorly understood. Proteasome substrates are conjugated with small proteins (tags) like ubiquitin and Fat10 to target them to the proteasome. It is unclear if the structural plasticity of proteasome-targeting tags influences substrate degradation. The tag Fat10 is activated during inflammation, and ambiguously, Fat10 and its substrates undergo rapid proteasomal degradation. We report that the rapid degradation of Fat10 substrates depends on its structural plasticity. While the ubiquitin tag is recycled at the proteasome, Fat10 is degraded with the substrate, and the mechanical unfolding kinetics of Fat10 regulates substrate degradation. Our studies reveal that long-range salt bridges are absent in the Fat10 structure, creating a plastic protein with partially unstructured regions suitable for proteasome engagement. Such a malleable structure also provides low resistance to mechanical unfolding and expedites proteasomal degradation. We also uncovered that the Fat10 plasticity destabilizes substrates significantly and creates partially unstructured regions in the substrate to enhance degradation. NMR-relaxation-derived order parameters and temperature dependence of chemical shifts identify the Fat10-induced partially unstructured regions in the substrate. They correlated excellently to the regions where Fat10 contacts the substrate, suggesting that the tag-substrate collision destabilizes the substrate. These results highlight a strong dependence of proteasomal degradation on the structural plasticity and thermodynamic properties of the proteasome-targeting tag.
Differential disruptions in population coding along the dorsal-ventral axis of CA1 in the APP/PS1 mouse model of Aβ pathology
Authors: Chockanthan Udaysankar , Padmanabhan Krishnan
Published: July 2022

Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder characterized by a range of behavioral alterations including memory loss as well as cognitive and psychiatric symptoms. While there is growing evidence that cellular and molecular pathologies, such as the accumulation of amyloid beta (Aβ) plaques may contribute to AD, it remains unclear how this histopathology can give rise to such disparate behavioral deficits. One hypothesis for these diverse behavioral presentations is that Aβ accumulation has differential effects on neuronal circuits across brain regions, depending on the diverse neurophysiological properties and connections within and between the neurons in these different areas. To test this, we recorded from large neuronal populations in the dorsal and ventral CA1 regions of the hippocampus, areas that are known to be structurally and functionally diverse, in both APP/PS1 animals, a mouse model of Aβ pathology, and age-matched C57BL/6 controls. Although we found similar levels of Aβ pathology in the two subregions, populations of neurons in dorsal and ventral CA1 in APP/PS1 mice showed distinct signatures of disrupted neuronal activity as animals navigated a virtual reality environment. In dorsal CA1, pairwise correlations and entropy, a measure of the diversity of activity patterns, were decreased in the APP/PS1 mice. However, in ventral CA1, the opposite findings were observed; pair-wise correlations and entropy was increased in APP/PS1 mice relative to C57BL/6 controls. When we attempted to connect the microscopic features of population activity (the correlations) with the macroscopic features of the population code (the entropy) using a pairwise Ising model, we found that the models’ performance decreased in predicting dorsal CA1 activity but increased in predicting vCA1 activity in APP/PS1 mice, as compared to the C57BL/6 animals. Taken together, these findings suggest that Aβ pathology exerts distinct effects across different hippocampal regions. Our results suggest that the diverse behavioral deficits associated with AD and the cellular pathology that arises from Aβ accumulation may be mechanistically linked by studying the dynamics of neural activity within these diverse hippocampal circuits.
Hippocampal blood flow rapidly and preferentially increases after a bout of moderate-intensity exercise in older adults with poor cerebrovascular health
Authors: Palmer Jacqueline A. , Morris Jill K , Billinger Sandra A. , Lepping Rebecca J , Martin Laura , Green Zachary , Vidoni Eric D.
Published: July 2022

Over the course of aging, there is an early degradation of cerebrovascular health that may be attenuated with aerobic exercise training. Yet, the acute cerebrovascular response to a single bout of exercise remains elusive, particularly within key brain regions most affected by age-related disease processes. We investigated the acute global and region-specific cerebral blood flow (CBF) response to 15 minutes of moderate-intensity aerobic exercise in older adults (≥65years) (n=60) using arterial spin labeling magnetic resonance imaging. Within 0-6 minutes post-exercise, CBF decreased across all regions, an effect that was attenuated in the hippocampus. The exercise-induced CBF drop was followed by a rebound effect over the 24-minute post-exercise assessment period, an effect that was most robust in the hippocampus. Individuals with low baseline perfusion demonstrated the greatest hippocampal-specific CBF effect post-exercise, showing no immediate drop and a rapid increase in CBF that exceeded baseline levels within 6-12 minutes post-exercise. Gains in domain-specific cognitive performance post-exercise were not associated with changes in regional CBF, suggesting dissociable effects of exercise on acute neural and vascular plasticity. Together, the present findings support a precision-medicine framework for the use of exercise to target brain health that carefully considers age-related changes in the cerebrovascular system.
Synthetic yeast chromosome XI design enables extrachromosomal circular DNA formation on demand
Authors: Blount Benjamin A , Lu Xinyu , Driessen Maureen R M , Jovicevic Dejana , Sanchez Mateo I , Ciurkot Klaudia , Zhao Yu , Lauer Stephanie , McKiernan Robert M , Gowers Glen-Oliver F , Sweeney Fiachra , Fanfani Viola , Lobzaev Evgenii , Palacios-Flores Kim , Walker Roy , Hesketh Andy , Oliver Stephen G , Cai Yizhi , Stracquadanio Giovanni , Mitchell Leslie A , Bader Joel S , Boeke Jef D , Ellis Tom
Published: July 2022

We describe construction of the 660 kilobase synthetic yeast chromosome XI (synXI) and reveal how synthetic redesign of non-coding DNA elements impact the cell. To aid construction from synthesized 5 to 10 kilobase DNA fragments, we implemented CRISPR-based methods for synthetic crossovers in vivo and used these methods in an extensive process of bug discovery, redesign and chromosome repair, including for the precise removal of 200 kilobases of unexpected repeated sequence. In synXI, the underlying causes of several fitness defects were identified as modifications to non-coding DNA, including defects related to centromere function and mitochondrial activity that were subsequently corrected. As part of synthetic yeast chromosome design, loxPsym sequences for Cre-mediated recombination are inserted between most genes. Using the GAP1 locus from chromosome XI, we show here that targeted insertion of these sites can be used to create extrachromosomal circular DNA on demand, allowing direct study of the effects and propagation of these important molecules. Construction and characterization of synXI has uncovered effects of non-coding and extrachromosomal circular DNA, contributing to better understanding of these elements and informing future synthetic genome design.
A broad, exposome-type evaluation of xenobiotic phase II biotransformation in human biofluids by LC-MS/MS
Authors: Fareed Yasmin , Braun Dominik , Flasch Mira , Globisch Daniel , Warth Benedikt
Published: July 2022

Xenobiotics are chemicals foreign to a specific organism that humans are exposed to on a daily basis through their food, drugs and the environment. These molecules are frequently metabolized to increase polarity and subsequent excretion. During sample preparation, deconjugation of phase II metabolites is a critical step to capture the total exposure to chemicals in liquid chromatography mass spectrometry assays (LC-MS). Knowledge on deconjugation efficiencies of different enzymes and the extend of conjugation in human biofluids has primarily been investigated for single compounds or individual chemical classes. In this study, the performance of three β-glucuronidase and arylsulfatase mixtures from H. pomatia, from recombinant sources (BGS™), and from Escherichia coli combined with recombinant arylsulfatase (ASPC™) was compared and the efficiency of phase II deconjugation was monitored in breast milk, urine and plasma. An innovative LC-MS/MS biomonitoring method encompassing more than 80 highly diverse xenobiotics (e.g., plasticizers, industrial chemicals, mycotoxins, phytoestrogens, pesticides) was utilized for the comprehensive investigation of phase II conjugation in experiments investigating levels in breast milk and urine obtained from breastfeeding women. Overall, it was confirmed that H. pomatia is the most efficient enzyme in hydrolyzing different classes of xenobiotics for future exposome-scale biomonitoring studies. The recombinant BGS™ formulation, however, provided better results for breast milk samples, primarily due to lower background contamination, a major issue when employing the typically applied crude H. pomatia extracts. A deeper understanding of the global xenobiotic conjugation patterns will be essential for capturing environmental and food-related exposures within the exposome framework more comprehensively.

Graphical abstract
Gibberellins promote polar auxin transport to regulate stem cell fate decisions in cambium
Authors: Mäkilä Riikka , Wybouw Brecht , Smetana Ondrej , Vainio Leo , Solé-Gil Anna , Lyu Munan , Ye Lingling , Wang Xin , Siligato Riccardo , Jenness Mark Kubo , Murphy Angus S. , Mähönen Ari Pekka
Published: July 2022

Vascular cambium contains bifacial stem cells, which produce secondary xylem to one side and secondary phloem to the other. However, how these fate decisions are regulated is unknown. Here, we show that the positioning of an auxin signalling maximum within the cambium determines the fate of stem cell daughters. The position is modulated by gibberellin-regulated, PIN1-dependent polar auxin transport. Gibberellin treatment broadens auxin maximum from the xylem side of the cambium towards the phloem. As a result, xylem-side stem cell daughter preferentially differentiates into xylem, while phloem-side daughter retains stem cell identity. Occasionally, this broadening leads to direct specification of both daughters as xylem, and consequently, adjacent phloem-identity cell reverts to being stem cell. Conversely, reduced gibberellin levels favour specification of phloem-side stem cell daughter as phloem. Together, our data provide a mechanism by which gibberellin regulates the ratio of xylem and phloem production.
Urban birds’ tolerance towards humans was largely unaffected by increased variation in human levels due to COVID-19 shutdowns
Authors: Mikula Peter , Bulla Martin , Blumstein Daniel T. , Benedetti Yanina , Floigl Kristina , Jokimäki Jukka , Kaisanlahti-Jokimäki Marja-Liisa , Markó Gábor , Morelli Federico , Møller Anders Pape , Siretckaia Anastasiia , Szakony Sára , Weston Michael A. , Zeid Farah Abou , Tryjanowski Piotr , Albrecht Tomáš
Published: July 2022

The coronavirus disease 2019 (COVID-19) pandemic dramatically altered human activities, and, during shutdowns. Here, we evaluated whether urban birds from five countries changed their tolerance towards humans during the COVID-19 shutdowns. We collected 6369 flight initiation distance estimates for 147 bird species and found that human numbers in parks (at a given hour, day, week or year - before and during the COVID-19 shutdowns) had a little effect on birds’ tolerance of approaching humans. Apart from the actual human numbers in the area (hourly scale), the effect of human activity at other temporal scales centered around zero. The results were similar across countries, for most species or when we restricted our analyses only to species sampled both before and during the COVID-19 shutdowns. As expected, the level of daily human presence in parks (measured by Google Mobility Reports) correlated negatively with the stringency of governmental restrictions (a weekly proxy for human presence) and was overall lower during COVID-19 shutdowns than during the post-shutdown year (2022). Our results highlight the resilience of birds to changes in human numbers on multiple temporal scales, the complexities of linking animal fear responses to human behavior, and the challenge of quantifying both simultaneouslyin situ.
FtsK, a DNA motor protein, coordinates the genome segregation and early cell division processes in Deinococcus radiodurans
Authors: Mishra Shruti , Misra Hari S. , Kota Swathi
Published: July 2022

FtsK/SpoIIIE protein family are DNA translocases known as the fastest DNA motor proteins that use ATP for their movement on DNA. Most of the studies in single chromosome-containing bacteria have established the role of FtsK in chromosome dimer resolution (CDR) connecting the bacterial chromosome segregation process with cell division. But, only limited reports are available on the interdependent regulation of genome segregation and cell division in multipartite genome harbouring (MGH) bacteria. In this study, for the first time, we report the characterization of FtsK from the radioresistant MGH bacterium Deinococcus radiodurans R1 (drFtsK). drFtsK shows the activity characteristics of a typical FtsK/SpoIIIE/Tra family. It stimulates the site-specific recombination catalyzed by Escherichia coli tyrosine recombinases. drFtsK interacts with various cell division and genome segregation proteins of D. radiodurans. Microscopic examination of different domain deletion mutants of this protein reveals alterations in cellular membrane architecture and nucleoid morphology. In-vivo localization studies of drFtsK-RFP show that it forms multiple foci on nucleoid as well as on the membrane with maximum density on the septum. drFtsK coordinates its movement with nucleoid separation. The alignment of its foci shifts from old to new septum indicating its cellular dynamics with the FtsZ ring during the cell division process. Nearly, similar positional dynamicity of FtsK was observed in cells recovering from gamma radiation exposure. These results suggest that FtsK forms a part of chromosome segregation, cell envelope, and cell division machinery in D. radiodurans.

Importance

Deinococcus radiodurans show extraordinary resistance to γ-radiation. It is polyploid and harbours a multipartite genome comprised of two chromosomes and two plasmids, packaged in a doughnut-shaped toroidal nucleoid. Very little is known about how the tightly packed genome is accurately segregated and the next divisional plane is determined. FtsK, a multifunctional protein, helps in pumping the septum-trapped DNA in several bacteria. Here, we characterized FtsK of D. radiodurans R1 (drFtsK) for the first time and showed it to be an active protein. The absence of drFtsK causes many defects in morphology at both cellular and nucleoid levels. The compact packaging of the deinococcal genome and cell membrane formation is hindered in ftsK mutants. In-vivo drFtsK is dynamic, forms foci on both nucleoid and septum, and coordinates with FtsZ for the next cell division. Thus, drFtsK role in maintaining the normal genome phenotype and cell division in Deinococcus radiodurans is suggested.
Allele-specific expression reveals multiple paths to highland adaptation in maize
Authors: Hu Haixiao , Crow Taylor , Nojoomi Saghi , Schulz Aimee J. , Hufford Matthew B. , Flint-Garcia Sherry , Sawers Ruairidh , Rellan-Alvarez Ruben , Estévez-Palmas Juan M. , Ross-Ibarra Jeffrey , Runcie Daniel E.
Published: July 2022

Maize is a staple food of smallholder farmers living in highland regions up to 4,000 meters above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggests the maize’s adaptation to these regions occurred largely independently, providing a case study for parallel evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele-specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence. Our findings reveal a complex genetic architecture of cis-regulatory alleles underlying adaptation to highlands in maize. Although the vast majority of evolutionary changes associated with highland adaptation were region-specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well.
Enhanced capillary pumping using open-channel capillary trees with integrated paper pads
Authors: Tokihiro Jodie C. , Tu Wan-chen , Berthier Jean , Lee Jing J. , Dostie Ashley M. , Khor Jian Wei , Eakman Madeleine , Theberge Ashleigh B. , Berthier Erwin
Published: July 2022

The search for efficient capillary pumping has led to two main directions for investigation: first, assembly of capillary channels to provide high capillary pressures, and second, imbibition in absorbing fibers or paper pads. In the case of open microfluidics (i.e., channels where the top boundary of the fluid is in contact with air instead of a solid wall), the coupling between capillary channels and paper pads unites the two approaches and provides enhanced capillary pumping. In this work, we investigate the coupling of capillary trees— networks of channels mimicking the branches of a tree—with paper pads placed at the extremities of the channels, mimicking the small capillary networks of leaves. It is shown that high velocities and flow rates (7 mm/s or 13.1 µL/s) for more than 30 seconds using 50% (v/v) isopropyl alcohol, which has a 3-fold increase in viscosity in comparison to water; 6.5 mm/s or 12.1 µL/s for more than 55 seconds with pentanol, which has an 3.75-fold increase in viscosity in comparison to water; >3.5 mm/s or 6.5 µL/s for more than 150 seconds with nonanol, which has an 11-fold increase in viscosity in comparison to water) can be reached in the root channel, enabling higher sustained flow rates than that of capillary trees alone.
ACtivE: Assembly and CRISPR-targeted in vivo Editing for Yeast Genome Engineering Using Minimum Reagents and Time
Authors: Malcı Koray , Jonguitud-Borrego Nestor , van der Straten Hugo , Puodžiūnaitė Urtė , Johnston Emily J. , Rosser Susan J. , Rios-Solis Leonardo
Published: July 2022

Among the numerous genetic tools developed for yeast, CRISPR/Cas system has been a widely used genome editing method thanks to its sophistication. However, CRISPR methods for yeast generally rely on pre-assembled DNAs and extra cloning steps to deliver gRNA, Cas protein, and donor DNA. These laborious steps might hinder its usefulness. Here, we propose a convenient, rapid, standardizable CRISPR method, named Assembly and CRISPR-targeted in vivo Editing (ACtivE), which only relies on in vivo assembly of linear DNA fragments for both plasmid and donor DNA construction. Thus, depending on the user’s need, these parts can be easily selected and combined from a repository, serving as a toolkit for rapid genome editing without any expensive reagent. The toolkit contains verified linear DNA fragments, which are easy to store, share and transport at room temperature, drastically reducing expensive shipping costs and assembly time. After optimizing this technique, eight ARS-close loci in the yeast genome were also characterized in terms of integration and gene expression efficiencies and the impacts of the disruptions of these regions on cell fitness. The flexibility and multiplexing capacity of the ACtivE were shown by constructing β-carotene pathway. In only a few days, > 80% integration efficiency for single gene integration and > 50% integration efficiency for triplex integration were achieved from scratch without using in vitro DNA assembly methods, restriction enzymes, or extra cloning steps. This study presents a standardizable method to be readily employed to accelerate yeast genome engineering and provides well-defined genomic location alternatives for yeast synthetic biology and metabolic engineering purposes.
Extended compartmental model for modeling COVID-19 epidemic in Slovenia
Authors: Fošnarič Miha , Kamenšek Tina , Gros Jerneja Žganec , Žibert Janez
Published: July 2022

In the absence of a systematic approach to epidemiological modeling in Slovenia, various isolated mathematical epidemiological models emerged shortly after the outbreak of the COVID-19 epidemic. We present an epidemiological model adapted to the COVID-19 situation in Slovenia. The standard SEIR model was extended to distinguish between age groups, symptomatic or asymptomatic disease progression, and vaccinated or unvaccinated populations. Evaluation of the model forecasts for 2021 showed the expected behavior of epidemiological modeling: our model adequately predicts the situation up to 4 weeks in advance; the changes in epidemiologic dynamics due to the emergence of a new viral variant in the population or the introduction of new interventions cannot be predicted by the model, but when the new situation is incorporated into the model, the forecasts are again reliable. Comparison with ensemble forecasts for 2022 within the European Covid-19 Forecast Hub showed better performance of our model, which can be explained by a model architecture better adapted to the situation in Slovenia, in particular a refined structure for vaccination, and better parameter tuning enabled by the more comprehensive data for Slovenia. Our model proved to be flexible, agile, and, despite the limitations of its compartmental structure, heterogeneous enough to provide reasonable and prompt short-term forecasts and possible scenarios for various public health strategies. The model has been fully operational on a daily basis since April 2020, served as one of the models for decision-making during the COVID-19 epidemic in Slovenia, and is part of the European Covid-19 Forecast Hub.
Highly multiplexed selection of RNA aptamers against a small molecule library
Authors: Townshend Brent , Kaplan Matias , Smolke Christina D.
Published: July 2022

Applications of synthetic biology spanning human health, industrial bioproduction, and ecosystem monitoring often require small molecule sensing capabilities, typically in the form of genetically encoded small molecule biosensors. Critical to the deployment of greater numbers of these systems are methods that support the rapid development of such biosensors against a broad range of small molecule targets. Here, we use a previously developed method for selection of RNA biosensors against unmodified small molecules (DRIVER) to perform a selection against a densely multiplexed mixture of small molecules, representative of those employed in high-throughput drug screening. Using a mixture of 5,120 target compounds randomly sampled from a large diversity drug screening library, we performed a 95-round selection and then analyzed the enriched RNA biosensor library using next generation sequencing (NGS). From our analysis, we identified RNA biosensors with at least 2-fold change in signal in the presence of at least 217 distinct target compounds with sensitivities down to 25 nM. Although many of these biosensors respond to multiple targets, clustering analysis indicated at least 150 different small-molecule sensing patterns. We also built a classifier that was able to predict whether the biosensors would respond to a new compound with an average precision of 0.82. Since the target compound library was designed to be representative of larger diversity compound libraries, we expect that the described approach can be used with similar compound libraries to identify aptamers against other small molecules with a similar success rate. The new RNA biosensors (or their component aptamers) described in this work can be further optimized and used in applications such as biosensing, gene control, or enzyme evolution. In addition, the data presented here provide an expanded compendium of new RNA aptamers compared to the 82 small molecule RNA aptamers published in the literature, allowing further bioinformatic analyses of the general classes of small molecules for which RNA aptamers can be found.