bluuebunny/crossref_metadata_2025 huggingface dataset:
Timing is everything: Early versus late palliative care consults in trauma
Authors: Spencer Audrey L. , Miller Preston R. , Russell Gregory B. , Cornea Isabella , Marterre Buddy
Published: January 2023

BACKGROUND

The incorporation of dedicated palliative care (PC) services in the care of the critically injured trauma patient is not yet universal. Preexisting data demonstrate both economic and clinical value of PC consults, yet patient selection and optimal timing of these consults are poorly defined, possibly leading to underutilization of PC services. Prior studies in geriatric patients have shown benefits of PC when PC clinicians are engaged earlier during hospitalization. We aim to compare hospitalization metrics of early versus late PC consultation in trauma patients.

METHODS

All patients 18 years or older admitted to the trauma service between January 1, 2019, and March 31, 2021, who received a PC consult were included. Patients were assigned to EARLY (PC consult ≤3 days after admission) and LATE (PC consult >3 days after admission) cohorts. Demographics, injury and underlying disease characteristics, outcomes, and financial data were compared. Length of stay (LOS) in the EARLY group is compared with LOS-3 in the LATE group.

RESULTS

A total of 154 patient records met the inclusion criteria (60 EARLY and 94 LATE). Injury Severity Score, head Abbreviated Injury Scale score, and medical comorbidities (congestive heart failure, dementia, previous stroke, chronic obstructive pulmonary disease, malignancy) were similar between the groups. The LATE group was younger (69.9 vs. 75.3, p = 0.04). Patients in the LATE group had significantly longer LOS (17.5 vs. 7.0 days, p < 0.01) and higher median hospital costs ($53,165 vs. $17,654, p < 0.01). Patients in the EARLY group had reduced ventilator days (2.4 vs. 7.0, p < 0.01) and reduced rates of tracheostomies and surgical feeding tubes (1.7% vs. 11.7%, p = 0.03).

CONCLUSION

Trauma patients with early PC consultation had shorter LOS, reduced ventilator days, reduced rates of invasive procedures, and lower costs even after correcting for delay to consult in the late group. These findings suggest the need for mechanisms leading to earlier PC consult in critically injured patients.

LEVEL OF EVIDENCE

Therapeutic/Care Management; Level IV.
A Validated Method to Identify Neuro-Ophthalmologists in a Large Administrative Claims Database
Authors: Feng Yilin , Lin Chun Chieh , Hamedani Ali G. , De Lott Lindsey B.
Published: January 2023

Background:

Validated methods to identify neuro-ophthalmologists in administrative data do not exist. The development of such method will facilitate research on the quality of neuro-ophthalmic care and health care utilization for patients with neuro-ophthalmic conditions in the United States.

Methods:

Using nationally representative, 20% sample from Medicare carrier files from 2018, we identified all neurologists and ophthalmologists billing at least 1 office-based evaluation and management (E/M) outpatient visit claim in 2018. To isolate neuro-ophthalmologists, the National Provider Identifier numbers of neuro-ophthalmologists in the North American Neuro-Ophthalmology Society (NANOS) directory were collected and linked to Medicare files. The proportion of E/M visits with International Classification of Diseases-10 diagnosis codes that best distinguished neuro-ophthalmic care (“neuro-ophthalmology–specific codes” or NSC) was calculated for each physician. Multiple logistic regression models assessed predictors of neuro-ophthalmology specialty designation after accounting for proportion of ophthalmology, neurology, and NSC claims and primary specialty designation. Sensitivity, specificity, and positive predictive value (PPV) for varying proportions of E/M visits with NSC were calculated.

Results:

We identified 32,293 neurologists and ophthalmologists who billed at least 1 outpatient E/M visit claim in 2018 in Medicare. Of the 472 NANOS members with a valid individual National Provider Identifier, 399 (84.5%) had a Medicare outpatient E/M visit in 2018. The model containing only the proportion of E/M visits with NSC best predicted neuro-ophthalmology specialty designation (odds ratio 1.05 [95% confidence interval 1.04, 1.05]; P < 0.001; area under the receiver operating characteristic [AUROC] = 0.91). Model predictiveness for neuro-ophthalmology designation was maximized when 6% of all billed claims were for NSC (AUROC = 0.89; sensitivity: 84.0%; specificity: 93.9%), but PPV was low (14.9%). The threshold was unchanged when limited only to neurologists billing ≥1% ophthalmology claims or ophthalmologists billing ≥1% neurology claims, but PPV increased (33.3%).

Conclusions:

Our study provides a validated method to identify neuro-ophthalmologists who can be further adapted for use in other administrative databases to facilitate future research of neuro-ophthalmic care delivery in the United States.
Prebiotic chemistry: a review of nucleoside phosphorylation and polymerization
Authors: Guo Xiaofan , Fu Songsen , Ying Jianxi , Zhao Yufen
Published: January 2023

The phosphorylation of nucleosides and their polymerization are crucial issues concerning the origin of life. The question of how these plausible chemical processes took place in the prebiotic Earth is still perplexing, despite several studies that have attempted to explain these prebiotic processes. The purpose of this article is to review these chemical reactions with respect to chemical evolution in the primeval Earth. Meanwhile, from our perspective, the chiral properties and selection of biomolecules should be considered in the prebiotic chemical origin of life, which may contribute to further research in this field to some extent.
Estimating the effect of COVID-19 on trial design characteristics: a registered report
Authors: Smith James A. , DeVito Nicholas , Lee Hopin , Tiplady Catherine , Abhari Roxanna E. , Kartsonaki Christiana
Published: January 2023

There have been reports of poor-quality research during the COVID-19 pandemic. This registered report assessed design characteristics of registered clinical trials for COVID-19 compared to non-COVID-19 trials to empirically explore the design of clinical research during a pandemic and how it compares to research conducted in non-pandemic times. We did a retrospective cohort study with a 1 : 1 ratio of interventional COVID-19 registrations to non-COVID-19 registrations, with four trial design outcomes: use of control arm, randomization, blinding and prospective registration. Logistic regression was used to estimate the odds ratio of investigating COVID-19 versus not COVID-19 and estimate direct and total effects of investigating COVID-19 for each outcome. The primary analysis showed a positive direct and total effect of COVID-19 on the use of control arms and randomization. It showed a negative direct effect of COVID-19 on blinding but no evidence of a total effect. There was no evidence of an effect on prospective registration. Taken together with secondary and sensitivity analyses, our findings are inconclusive but point towards a higher prevalence of key design characteristics in COVID-19 trials versus controls. The findings do not support much existing COVID-19 research quality literature, which generally suggests that COVID-19 led to a reduction in quality. Limitations included some data quality issues, minor deviations from the pre-registered plan and the fact that trial registrations were analysed which may not accurately reflect study design and conduct. Following in-principle acceptance, the approved stage 1 version of this manuscript was pre-registered on the Open Science Framework athttps://doi.org/10.17605/OSF.IO/5YAEB. This pre-registration was performed prior to data analysis.
Effects of temporal properties of facial expressions on the perceived intensity of emotion
Authors: Harada Yuki , Ohyama Junji , Wada Makoto
Published: January 2023

A series of multiple facial expressions can be temporally perceived as an averaged facial expression in a process known as ensemble perception. This study examined the effect of temporal parameters on the perceived intensity of facial expression in each emotion, and how the effect varies with autistic traits in typically developing people. In the experiment, we presented facial expressions that switched from emotional to neutral expressions, and vice versa, for 3 s. Participants rated the overall perceived intensity of the facial emotions as a whole rather than rating individual items within the set. For the two tasks, a ratio of duration of emotional faces to duration of neutral faces (emotional ratio) and the timing for transitions were manipulated individually. The results showed that the intensity of facial emotion was perceived more strongly when the presentation ratio increased and when the emotional expression was presented last. The effects were different among the emotions (e.g. relatively weak in the anger expression). Moreover, the perceived intensity of angry expressions decreased with autistic traits. These results suggest that the properties and individual differences in the facial ensemble of each emotion affect emotional perceptions.
How keratin cortex thickness affects iridescent feather colours
Authors: Jeon Deok-Jin , Ji Seungmuk , Lee Eunok , Kang Jihun , Kim Jiyeong , D'Alba Liliana , Manceau Marie , Shawkey Matthew D. , Yeo Jong-Souk
Published: January 2023

The bright, saturated iridescent colours of feathers are commonly produced by single and multi-layers of nanostructured melanin granules (melanosomes), air and keratin matrices, surrounded by an outer keratin cortex of varying thicknesses. The role of the keratin cortex in colour production remains unclear, despite its potential to act as a thin film or absorbing layer. We use electron microscopy, optical simulations and oxygen plasma-mediated experimental cortex removal to show that differences in keratin cortex thickness play a significant role in producing colours. The results indicate that keratin cortex thickness determines the position of the major reflectance peak (hue) from nanostructured melanosomes of common pheasant (
Phasianus colchicus
) feathers. Specifically, the common pheasant has appropriate keratin cortex thickness to produce blue and green structural colours. This finding identifies a general principle of structural colour production and sheds light on the processes that shaped the evolution of brilliant iridescent colours in the common pheasant.
Multi-scale modelling of fatigue crack propagation due to liquid droplet impingement
Authors: Ganesh Kona Veera , Islam Md Rushdie Ibne , Kumar Patra Puneet , Patrick Travis Karl
Published: January 2023

We develop a sequential multi-scaling framework for studying the problem of fatigue crack propagation due to liquid droplet impingement. The scope is limited to a hypothetical material and a hypothetical liquid. The multi-scaling is achieved by handshaking the atomistic scale molecular dynamics (MD) simulations with the continuum scale smoothed particle hydrodynamics (SPH). The handshaking, in turn, is performed by evaluating the material, the fracture and the loading properties from MD simulations, and using them as inputs in the continuum scale SPH model. Due to the qualitative agreement of the pressure developed in the fluid and the substrate between the MD simulations and already published results, the liquid droplet impact in SPH is simulated through appropriate surface stresses. Further, we incorporate the pseudo-spring approach within the SPH model to develop a methodology for studying mixed-mode fatigue crack propagation. Our methodology provides good agreement with the existing literature for several cases. Lastly, we calculate the fatigue life of an edge-cracked specimen due to liquid droplet impingement.
Planning spatial networks with Monte Carlo tree search
Authors: Darvariu Victor-Alexandru , Hailes Stephen , Musolesi Mirco
Published: January 2023

We tackle the problem of goal-directed graph construction: given a starting graph, finding a set of edges whose addition maximally improves a global objective function. This problem emerges in many transportation and infrastructure networks that are of critical importance to society. We identify two significant shortcomings of present reinforcement learning methods: their exclusive focus on topology to the detriment of spatial characteristics (which are known to influence the growth and density of links), as well as the rapid growth in the action spaces and costs of model training. Our formulation as a deterministic Markov decision process allows us to adopt the Monte Carlo tree search framework, an artificial intelligence decision-time planning method. We propose improvements over the standard upper confidence bounds for trees (UCT) algorithm for this family of problems that addresses their single-agent nature, the trade-off between the cost of edges and their contribution to the objective, and an action space linear in the number of nodes. Our approach yields substantial improvements over UCT for increasing the efficiency and attack resilience of synthetic networks and real-world Internet backbone and metro systems, while using a wall clock time budget similar to other search-based algorithms. We also demonstrate that our approach scales to significantly larger networks than previous reinforcement learning methods, since it does not require training a model.
Observed and dark diversity dynamics over millennial time scales: fast life-history traits linked to expansion lags of plants in northern Europe
Authors: Trindade Diego P. F. , Carmona Carlos P. , Reitalu Triin , Pärtel Meelis
Published: January 2023

Global change drivers (e.g. climate and land use) affect the species and functional traits observed in a local site but also its dark diversity—the set of species and traits locally suitable but absent. Dark diversity links regional and local scales and, over time, reveals taxa under expansion lags by depicting the potential biodiversity that remains suitable but is absent locally. Since global change effects on biodiversity are both spatially and temporally scale dependent, examining long-term temporal dynamics in observed and dark diversity would be relevant to assessing and foreseeing biodiversity change. Here, we used sedimentary pollen data to examine how both taxonomic and functional observed and dark diversity changed over the past 14 500 years in northern Europe. We found that taxonomic and functional observed and dark diversity increased over time, especially after the Late Glacial and during the Late Holocene. However, dark diversity dynamics revealed expansion lags related to species' functional characteristics (dispersal limitation and stress intolerance) and an extensive functional redundancy when compared to taxa in observed diversity. We highlight that assessing observed and dark diversity dynamics is a promising tool to examine biodiversity change across spatial scales, its possible causes, and functional consequences.
Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents
Authors: Chou Pei-Hsuan , Hu Marian Y. , Guh Ying-Jey , Wu Guan-Chung , Yang Shan-Hua , Tandon Kshitij , Shao Yi-Ta , Lin Li-Yih , Chen Chi , Tseng Kuang-Yu , Wang Min-Chen , Zhang Cheng-Mao , Han Bor-Cheng , Lin Ching-Chun , Tang Sen-Lin , Jeng Ming-Shiou , Chang Ching-Fong , Tseng Yung-Che
Published: January 2023

The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is
Xenograpsus testudinatus,
a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide,
X. testudinatus
occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of
X. testudinatus
that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by
Epsilonproteobacteria
. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.
Neuromodulation and differential learning across mosquito species
Authors: Wolff Gabriella H. , Lahondère Chloé , Vinauger Clément , Rylance Elizabeth , Riffell Jeffrey A.
Published: January 2023

Mosquitoes can change their feeding behaviours based on past experiences, such as shifting from biting animals to biting humans or avoiding defensive hosts (Wolff & Riffell 2018
J. Exp. Biol.
221
, jeb157131. (
doi:10.1242/jeb.157131
)). Dopamine is a critical neuromodulator for insects, allowing flexibility in their feeding preferences, but its role in the primary olfactory centre, the antennal lobe (AL), remains unclear (Vinauger
et al.
2018
Curr. Biol.
28
, 333–344.e8. (
doi:10.1016/j.cub.2017.12.015
)). It is also unknown whether mosquitoes can learn some odours and not others, or whether different species learn the same odour cues. We assayed aversive olfactory learning in four mosquito species with different host preferences, and found that they differentially learn odours salient to their preferred host. Mosquitoes that prefer humans learned odours found in mammalian skin, but not a flower odour, and a nectar-feeding species only learned a floral odour. Comparing the brains of these four species revealed significantly different innervation patterns in the AL by dopaminergic neurons. Calcium imaging in the
Aedes aegypti
AL and three-dimensional image analyses of dopaminergic innervation show that glomeruli tuned to learnable odours have significantly higher dopaminergic innervation. Changes in dopamine expression in the insect AL may be an evolutionary mechanism to adapt olfactory learning circuitry without changing brain structure and confer to mosquitoes an ability to adapt to new hosts.
Landscape-scale forest cover drives the predictability of forest regeneration across the Neotropics
Authors: Arroyo-Rodríguez Víctor , Rito Kátia F. , Farfán Michelle , Navia Iván C. , Mora Francisco , Arreola-Villa Felipe , Balvanera Patricia , Bongers Frans , Castellanos-Castro Carolina , Catharino Eduardo L. M. , Chazdon Robin L. , Dupuy-Rada Juan M. , Ferguson Bruce G. , Foster Paul F. , González-Valdivia Noel , Griffith Daniel M. , Hernández-Stefanoni José L. , Jakovac Catarina C. , Junqueira André B. , Jong Bernardus H. J. , Letcher Susan G. , May-Pat Filogonio , Meave Jorge A. , Ochoa-Gaona Susana , Meirelles Gabriela S. , Muñiz-Castro Miguel A. , Muñoz Rodrigo , Powers Jennifer S. , Rocha Gustavo P. E. , Rosário Ricardo P. G. , Santos Bráulio A. , Simon Marcelo F. , Tabarelli Marcelo , Tun-Dzul Fernando , van den Berg Eduardo , Vieira Daniel L. M. , Williams-Linera Guadalupe , Martínez-Ramos Miguel
Published: January 2023

Abandonment of agricultural lands promotes the global expansion of secondary forests, which are critical for preserving biodiversity and ecosystem functions and services. Such roles largely depend, however, on two essential successional attributes, trajectory and recovery rate, which are expected to depend on landscape-scale forest cover in nonlinear ways. Using a multi-scale approach and a large vegetation dataset (843 plots, 3511 tree species) from 22 secondary forest chronosequences distributed across the Neotropics, we show that successional trajectories of woody plant species richness, stem density and basal area are less predictable in landscapes (4 km radius) with intermediate (40–60%) forest cover than in landscapes with high (greater than 60%) forest cover. This supports theory suggesting that high spatial and environmental heterogeneity in intermediately deforested landscapes can increase the variation of key ecological factors for forest recovery (e.g. seed dispersal and seedling recruitment), increasing the uncertainty of successional trajectories. Regarding the recovery rate, only species richness is positively related to forest cover in relatively small (1 km radius) landscapes. These findings highlight the importance of using a spatially explicit landscape approach in restoration initiatives and suggest that these initiatives can be more effective in more forested landscapes, especially if implemented across spatial extents of 1–4 km radius.
Rapid evolution of unimodal but not of linear thermal performance curves inDaphnia magna
Authors: Wang Ying-Jie , Tüzün Nedim , De Meester Luc , Feuchtmayr Heidrun , Sentis Arnaud , Stoks Robby
Published: January 2023

Species may cope with warming through both rapid evolutionary and plastic responses. While thermal performance curves (TPCs), reflecting thermal plasticity, are considered powerful tools to understand the impact of warming on ectotherms, their rapid evolution has been rarely studied for multiple traits. We capitalized on a 2-year experimental evolution trial in outdoor mesocosms that were kept at ambient temperatures or heated 4°C above ambient, by testing in a follow-up common-garden experiment, for rapid evolution of the TPCs for multiple key traits of the water fleaDaphnia magna. The heat-selectedDaphniashowed evolutionary shifts of the unimodal TPCs for survival, fecundity at first clutch and intrinsic population growth rate toward higher optimum temperatures, and a less pronounced downward curvature indicating a better ability to keep fitness high across a range of high temperatures. We detected no evolution of the linear TPCs for somatic growth, mass and development rate, and for the traits related to energy gain (ingestion rate) and costs (metabolic rate). As a result, also the relative thermal slope of energy gain versus energy costs did not vary. These results suggest the overall (rather thanper capita) top-down impact ofD. magnamay increase under rapid thermal evolution.
Molecular elements: novel approaches for molecular building
Authors: Wang Ruowen , Wang Xueqiang , Xie Sitao , Zhang Yanyan , Ji Dingkun , Zhang Xiaobing , Cui Cheng , Jiang Jianhui , Tan Weihong
Published: January 2023

Classically, a molecular element (ME) is a pure substance composed of two or more atoms of the same element. However, MEs, in the context of this review, can be any molecules as elements bonded together into the backbone of synthetic oligonucleotides (ONs) with designed sequences and functions, including natural A, T, C, G, U, and unnatural bases. The use of MEs can facilitate the synthesis of designer molecules and smart materials. In particular, we discuss the landmarks associated with DNA structure and related technologies, as well as the extensive application of ONs, the ideal type of molecules for intervention therapy aimed at correcting disease-causing genetic errors (indels). It is herein concluded that the discovery of ON therapeutics and the fabrication of designer molecules or nanostructures depend on the ME concept that we previously published. Accordingly, ME will be our focal point as we discuss related research directions and perspectives in making molecules and materials.

This article is part of the theme issue ‘Reactivity and mechanism in chemical and synthetic biology’.
Rethinking nucleic acids from their origins to their applications
Authors: Benner Steven A.
Published: January 2023

Reviewed are three decades of synthetic biology research in our laboratory that has generated alternatives to standard DNA and RNA as possible informational systems to support Darwinian evolution, and therefore life, and to understand their natural history, on Earth and throughout the cosmos. From this, we have learned that:

•

the core structure of nucleic acids appears to be a natural outcome of non-biological chemical processes probably in constrained, intermittently irrigated, sub-aerial aquifers on the surfaces of rocky planets like Earth and/or Mars approximately 4.36 ± 0.05 billion years ago;

•

however, this core is not unique. Synthetic biology has generated many different molecular systems able to support the evolution of molecular information;

•

these alternatives to standard DNA and RNA support biotechnology, including DNA synthesis, human diagnostics, biomedical research and medicine;

•

in particular, they support laboratory
in vitro
evolution (LIVE) with performance to generate catalysts at least 10
4
–10
5
fold better than standard DNA libraries, enhancing access to receptors and catalysts on demand. Coupling nanostructures to the products of LIVE with expanded DNA offers new approaches for disease therapy; and

•

nevertheless, a polyelectrolyte structure and size regular building blocks are required for
any
informational polymer to support Darwinian evolution. These features serve as universal and agnostic biosignatures, useful for seeking life throughout the Solar System.

This article is part of the theme issue ‘Reactivity and mechanism in chemical and synthetic biology’.
Perseverance of protein homeostasis despite mistranslation of glycine codons with alanine
Authors: Hasan Farah , Lant Jeremy T. , O'Donoghue Patrick
Published: January 2023

By linking amino acids to their codon assignments, transfer RNAs (tRNAs) are essential for protein synthesis and translation fidelity. Some human tRNA variants cause amino acid mis-incorporation at a codon or set of codons. We recently found that a naturally occurring tRNA
Ser
variant decodes phenylalanine codons with serine and inhibits protein synthesis. Here, we hypothesized that human tRNA variants that misread glycine (Gly) codons with alanine (Ala) will also disrupt protein homeostasis. The A3G mutation occurs naturally in tRNA
Gly
variants (tRNA
Gly
CCC
, tRNA
Gly
GCC
) and creates an alanyl-tRNA synthetase (AlaRS) identity element (G3 : U70). Because AlaRS does not recognize the anticodon, the human tRNA
Ala
AGC
G35C (tRNA
Ala
ACC
) variant may function similarly to mis-incorporate Ala at Gly codons. The tRNA
Gly
and tRNA
Ala
variants had no effect on protein synthesis in mammalian cells under normal growth conditions; however, tRNA
Gly
GCC
A3G depressed protein synthesis in the context of proteasome inhibition. Mass spectrometry confirmed Ala mistranslation at multiple Gly codons caused by the tRNA
Gly
GCC
A3G and tRNA
Ala
AGC
G35C mutants, and in some cases, we observed multiple mistranslation events in the same peptide. The data reveal mistranslation of Ala at Gly codons and defects in protein homeostasis generated by natural human tRNA variants that are tolerated under normal conditions.

This article is part of the theme issue ‘Reactivity and mechanism in chemical and synthetic biology’.
Genome mining of cryptic bisabolenes that were biosynthesized by intramembrane terpene synthases from
Antrodia cinnamomea
Authors: Hewage Ranuka T. , Tseng Cheng-Chung , Liang Suh-Yuen , Lai Chen-Yu , Lin Hsiao-Ching
Published: January 2023

Terpenoids represent the largest structural family of natural products (NPs) and have various applications in the pharmaceutical, food and fragrance industries. Their diverse scaffolds are generated via a multi-step cyclization cascade of linear isoprene substrates catalysed by terpene synthases (TPSs). Bisabolene NPs, which are sesquiterpenes (C15), have wide applications in medicines and biofuels and serve as bioactive substances in ecology. Despite the discovery of some canonical class I TPSs that synthesize bisabolenes from plants, bacteria and insects, it remained unknown whether any bisabolene synthases from fungi could produce bisabolenes as a main product.
Antrodia cinnamomea
, a Basidiomycota fungus, is a medicinal mushroom indigenous to Taiwan and a known prolific producer of bioactive terpenoids, but little is known regarding the enzymes involved in the biosynthetic pathways. Here, we applied a genome mining approach against
A. cinnamomea
and discovered two non-canonical UbiA-type TPSs that both synthesize (+)-(
S
,
Z
)-α-bisabolene (
1
). It was determined that two tailoring enzymes, a P450 monooxygenase and a methyltransferase, install a C14-methyl ester on the bisabolene scaffold. In addition, four new bisabolene derivatives,
2
and
4
–
6
, were characterized from heterologous reconstitution in
Saccharomyces cerevisiae
. Our study uncovered enzymatic tools to generate structurally diverse bisabolene NPs.

This article is part of the theme issue ‘Reactivity and mechanism in chemical and synthetic biology’.
Ribosomal incorporation of negatively charged
d
-α- and
N
-methyl-
l
-α-amino acids enhanced by EF-Sep
Authors: Katoh Takayuki , Suga Hiroaki
Published: January 2023

Ribosomal incorporation of
d
-α-amino acids (
d
AA) and
N
-methyl-
l
-α-amino acids (
Me
AA) with negatively charged sidechains, such as
d
-Asp,
d
-Glu,
Me
Asp and
Me
Glu, into nascent peptides is far more inefficient compared to those with neutral or positively charged ones. This is because of low binding affinity of their aminoacyl-transfer RNA (tRNA) to elongation factor-thermo unstable (EF-Tu), a translation factor responsible for accommodation of aminoacyl-tRNA onto ribosome. It is well known that EF-Tu binds to two parts of aminoacyl-tRNA, the amino acid moiety and the T-stem; however, the amino acid binding pocket of EF-Tu bearing Glu and Asp causes electric repulsion against the negatively charged amino acid charged on tRNA. To circumvent this issue, here we adopted two strategies: (i) use of an EF-Tu variant, called EF-Sep, in which the Glu216 and Asp217 residues in EF-Tu are substituted with Asn216 and Gly217, respectively; and (ii) reinforcement of the T-stem affinity using an artificially developed chimeric tRNA, tRNA
Pro1E2
, whose T-stem is derived from
Escherichia coli
tRNA
Glu
that has high affinity to EF-Tu. Consequently, we could successfully enhance the incorporation efficiencies of
d
-Asp,
d
-Glu,
Me
Asp and
Me
Glu and demonstrated for the first time, to our knowledge, ribosomal synthesis of macrocyclic peptides containing multiple
d
-Asp or
Me
Asp.

This article is part of the theme issue ‘Reactivity and mechanism in chemical and synthetic biology’.
Structure, mechanism and inhibition of anthranilate phosphoribosyltransferase
Authors: Scully Thomas W. , Jiao Wanting , Mittelstädt Gerd , Parker Emily J.
Published: January 2023

Anthranilate phosphoribosyltransferase catalyses the second reaction in the biosynthesis of tryptophan from chorismate in microorganisms and plants. The enzyme is homodimeric with the active site located in the hinge region between two domains. A range of structures in complex with the substrates, substrate analogues and inhibitors have been determined, and these have provided insights into the catalytic mechanism of this enzyme. Substrate 5-phospho-
d
-ribose 1-diphosphate (PRPP) binds to the C-terminal domain and coordinates to Mg
2+
, in a site completed by two flexible loops. Binding of the second substrate anthranilate is more complex, featuring multiple binding sites along an anthranilate channel. This multi-modal binding is consistent with the substrate inhibition observed at high concentrations of anthranilate. A series of structures predict a dissociative mechanism for the reaction, similar to the reaction mechanisms elucidated for other phosphoribosyltransferases. As this enzyme is essential for some pathogens, efforts have been made to develop inhibitors for this enzyme. To date, the best inhibitors exploit the multiple binding sites for anthranilate.

This article is part of the theme issue ‘Reactivity and mechanism in chemical and synthetic biology’.
The DNA relaxation-dependent OFF-to-ON biasing of the type 1 fimbrial genetic switch requires the Fis nucleoid-associated protein
Authors: Conway Colin , Beckett Michael C. , Dorman Charles J.
Published: January 2023

The structural genes expressing type 1 fimbriae in

Escherichia coli

alternate between expressed (phase ON) and non-expressed (phase OFF) states due to inversion of the 314 bp fimS genetic switch. The FimB tyrosine integrase inverts fimS by site-specific recombination, alternately connecting and disconnecting the fim operon, encoding the fimbrial subunit protein and its associated secretion and adhesin factors, to and from its transcriptional promoter within fimS. Site-specific recombination by the FimB recombinase becomes biased towards phase ON as DNA supercoiling is relaxed, a condition that occurs when bacteria approach the stationary phase of the growth cycle. This effect can be mimicked in exponential phase cultures by inhibiting the negative DNA supercoiling activity of DNA gyrase. We report that this bias towards phase ON depends on the presence of the Fis nucleoid-associated protein. We mapped the Fis binding to a site within the invertible fimS switch by DNase I footprinting. Disruption of this binding site by base substitution mutagenesis abolishes both Fis binding and the ability of the mutated switch to sustain its phase ON bias when DNA is relaxed, even in bacteria that produce the Fis protein. In addition, the Fis binding site overlaps one of the sites used by the Lrp protein, a known directionality determinant of fimS inversion that also contributes to phase ON bias. The Fis–Lrp relationship at fimS is reminiscent of that between Fis and Xis when promoting DNA relaxation-dependent excision of bacteriophage λ from the

E. coli

chromosome. However, unlike the co-binding mechanism used by Fis and Xis at λ attR, the Fis–Lrp relationship at fimS involves competitive binding. We discuss these findings in the context of the link between fimS inversion biasing and the physiological state of the bacterium.
Vaccine effectiveness against SARS-CoV-2 Delta and Omicron infection and infectiousness within households in the Netherlands between July 2021 and August 2022
Authors: Hoeve Christina E. , de Gier Brechje , Huiberts Anne J. , de Melker Hester E. , Hahné Susan J.M. , van den Hof Susan , Knol Mirjam J.
Published: January 2023

Introduction

We aimed to estimate vaccine effectiveness against infection (VE- infection) and infectiousness (VE-infectiousness) in a household setting during Delta and Omicron. Knowing these effects can aid policy makers in deciding which groups to prioritize for vaccination.

Methods

Participants with a positive SARS-CoV-2 test were asked about COVID-19 vaccination status and SARS-CoV-2 testing of their household members one month later. VE-infection and VE-infectiousness was estimated using GEE logistic regression adjusting for age and vaccination status, calendar week and household size.

Results

3,409 questionnaires concerning 4,123 household members were included. During the Delta-period, VE-infection of primary series was 47% (95% CI: −27%-78%) and VE-infectiousness of primary series was 70% (95% CI: 28%-87%). During the Omicron-period, VE-infection was −36% (95% CI: −88%-1%) for primary series and −30% (95% CI: −80%-6%) for booster vaccination. The VE-infectiousness was 45% (95% CI: −14%-74%) for primary series and 64% (95% CI: 31%-82%) for booster vaccination.

Discussion

Our study shows that COVID-19 vaccination is effective against infection with SARS-CoV-2 Delta and against infectiousness of SARS-CoV-2 Delta and Omicron. Estimation of VE against infection with SARS-CoV-2 Omicron was limited by several factors. Our results support vaccination for those in close contact with vulnerable people to prevent transmission.
Assessment of AlphaFold structures and optimization methods for virtual screening
Authors: Peng Yanfei , Wu Xia , Lin Liang , Deng Zhiluo , Zhao Limin , Ke Hao
Published: January 2023

Recent advancements in artificial intelligence such as AlphaFold, have enabled more accurate prediction of protein three-dimensional structure from amino acid sequences. This has attracted significant attention, especially for the application of AlphaFold in drug discovery. However, how to take full advantage of AlphaFold to assist with virtual screening remains elusive. We evaluate the AlphaFold structures of 51 selected targets from the DUD-E database in virtual screening. Our analyses show that the virtual screening performance of about 35% of the AlphaFold structures is equivalent to that of DUD-E structures, and about 25% of the AlphaFold structures yield better results than the DUD-E structures. Remarkably, AlphaFold structures produce slightly better results than the Apo structures. Moreover, we develop a new consensus scoring method based on Z-score standardization and exponential function, which shows improved screening performance compared to traditional scoring methods. By implementing a multi-stage virtual screening process and the new consensus scoring method, we are able to improve the speed of virtual screening by about nine times without compromising the enrichment factor. Overall, our results provide insights into the potential use of AlphaFold in drug discovery and highlight the value of consensus scoring and multi-stage virtual screening.
Heritable microbiome variation is correlated with source environment in locally adapted maize varieties
Authors: He Xiaoming , Wang Danning , Jiang Yong , Li Meng , Delgado-Baquerizo Manuel , McLaughlin Chloee , Marcon Caroline , Guo Li , Baer Marcel , Moya Yudelsy A.T. , Wirén Nicolaus von , Deichmann Marion , Schaaf Gabriel , Piepho Hans-Peter , Yang Zhikai , Yang Jinliang , Yim Bunlong , Smalla Kornelia , Goormachtig Sofie , de Vries Franciska T. , Hüging Hubert , Sawers Ruairidh J. H. , Reif Jochen C. , Hochholdinger Frank , Chen Xinping , Yu Peng
Published: January 2023

Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbe interactions in the face of environmental stress. Here, we surveyed the root and rhizosphere microbiome of 129 accessions of locally adaptedZea mays, sourced from diverse habitats and grown under control and different stress conditions. We quantified treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome composition. Genome wide association analysis identified host genetic variants linked to both rhizosphere microbiome composition and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone microbeMassiliaand source total soil nitrogen, finding mutant plants to show a reduction in lateral root density. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.
Photosynthetic and water transport strategies of plants along a tropical forest aridity gradient: a test of optimality theory
Authors: Zhang-Zheng Huanyuan , Malhi Yadvinder , Gvozdevaite Agne , Peprah Theresa , Boakye Mickey , Ziemińska Kasia , Adu-Bredu Stephen , Aguirre-Gutiérrez Jesús , Sandoval David , Prentice Iain Colin , Menor Imma Oliveras
Published: January 2023

(1)

The research conducted, including the rationale

The direct effect of aridity on photosynthetic and water-transport strategies is not easy to discern in global analyses because of large-scale correlations between precipitation and temperature. We analyze tree traits collected along an aridity gradient in Ghana, West Africa that shows little temperature variation, in an attempt to disentangle thermal and hydraulic influences on plant traits.

(2)

Methods

Predictions derived from optimality theory on the variation of key plant traits along the aridity gradient are tested with field measurements.

(3)

results

Most photosynthetic traits show trends consistent with optimality-theory predictions, including higher photosynthetic capacity in the drier sites, and an association of higher photosynthetic capacity with greater respiration rates and greater water transport. Hydraulic traits show less consistency with theory or global-scale pattern, especially predictions based on xylem efficiency-safety tradeoff. Nonetheless, the link between photosynthesis and water transport still holds: species (predominantly deciduous species found in drier sites) with both higher sapwood-to-leaf area ratio (AS/AL) and potential hydraulic conductivity (Kp), implying higher transpiration, tend to have both higher photosynthetic capacity and lower leaf-internal CO2.

(4)

Conclusions

These results indicate that aridity is an independent driver of spatial patterns of photosynthetic traits, while plants show a diversity of water-transport strategies along the aridity gradient.

Plain language summary

Along an aridity gradient in Ghana, West-Africa, we used optimality theory to explain that aridity is an important driver of photosynthetic traits, independent of temperature. Toward drier sites, plants have higher photosynthetic capacities per leaf area but have fewer leaves. We also explain how plants arrange water transportation to support quicker photosynthesis at drier sites. However, plants at the drier sites seem to have diverse combinations of hydraulic traits to satisfy the need for photosynthesis. We reported surprising data-theory inconsistency for some hydraulic traits along the aridity gradient where further research is needed.
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence
Authors: Zhang Shuming , Yuan Long , Danilova Ludmila , Mo Guanglan , Zhu Qingfeng , Deshpande Atul , Bell Alexander T.F. , Elisseeff Jennifer , Popel Aleksander S. , Anders Robert A. , Jaffee Elizabeth M. , Yarchoan Mark , Fertig Elana J. , Kagohara Luciane T.
Published: January 2023

Novel immunotherapy combination therapies have improved outcomes for patients with hepatocellular carcinoma (HCC), but responses are limited to a subset of patients and recurrence can also occur. Little is known about the inter- and intra-tumor heterogeneity in cellular signaling networks within the HCC tumor microenvironment (TME) that underlie responses to modern systemic therapy. We applied spatial transcriptomics (ST) profiling to characterize the tumor microenvironment in HCC resection specimens from a clinical trial of neoadjuvant cabozantinib, a multi-tyrosine kinase inhibitor that primarily blocks VEGF, and nivolumab, a PD-1 inhibitor in which 5 out of 15 patients were found to have a pathologic response. ST profiling demonstrated that the TME of responding tumors was enriched for immune cells and cancer associated fibroblasts (CAF) with pro-inflammatory signaling relative to the non-responders. The enriched cancer-immune interactions in responding tumors are characterized by activation of the PAX5 module, a known regulator of B cell maturation, which colocalized with spots with increased B cell markers expression suggesting strong activity of these cells. Cancer-CAF interactions were also enriched in the responding tumors and were associated with extracellular matrix (ECM) remodeling as there was high activation of FOS and JUN in CAFs adjacent to tumor. The ECM remodeling is consistent with proliferative fibrosis in association with immune-mediated tumor regression. Among the patients with major pathologic response, a single patient experienced early HCC recurrence. ST analysis of this clinical outlier demonstrated marked tumor heterogeneity, with a distinctive immune-poor tumor region that resembles the non-responding TME across patients and was characterized by cancer-CAF interactions and expression of cancer stem cell markers, potentially mediating early tumor immune escape and recurrence in this patient. These data show that responses to modern systemic therapy in HCC are associated with distinctive molecular and cellular landscapes and provide new targets to enhance and prolong responses to systemic therapy in HCC.
A multivariate network analysis of ring- and diffuse-porous tree xylem vasculature segmented by convolutional neural networks
Authors: Huber Annika Erika , Haft-Javaherian Mohammad , Berg Maxime , Lanba Asheesh , Lorthois Sylvie , Bauerle Taryn L. , Nishimura Nozomi
Published: January 2023

The xylem network, the water conduction system in wood determines the ability of trees to avoid hydraulic failure during drought stress. The capability to withstand embolisms, disruptions of the water column by gas bubbles that contribute to hydraulic failure, is mainly determined by the anatomical arrangement and connectedness (topology) of xylem vessels. However, the quantification of xylem network characteristics has been difficult, so that relating network properties and topology to hydraulic vulnerability and predicting xylem function remains challenging. We studied the xylem vessel networks of three diffuse- (Fagus sylvatica, Liriodendron tulipifera, Populus x canadensis) and three ring-porous (Carya ovata, Fraxinus pennsylvatica, Quercus montana) tree species using volumetric images of xylem from laser ablation tomography (LATscan). Using convolutional neural networks for image segmentation, we generated three-dimensional, high-resolution maps of xylem vessels, with detailed measurements of morphology and topology. We studied the network topologies by incorporating multiple network metrics into a multidimensional analysis and simulated the robustness of these networks against the loss of individual vessel elements that mimic the obstruction of water flow from embolisms. This analysis suggested that networks inPopulus x canadensisandCarya ovataare quite similar despite being different wood types. Similar networks had comparable experimental measurements of P50 values (pressure inducing 50% hydraulic conductivity loss) obtained from hydraulic vulnerability curves, a common tool to quantify the cavitation resistance of xylem networks. This work produced novel data on plant xylem vessel networks and introduces new methods for analyzing the biological impact of these network structures.

Significance statement

The resilience of fluid transport networks such as xylem vessels that conduct water in trees depends on both the structure of the network and features of the individual network elements. High-resolution reconstruction of xylem networks from six tree species provided novel, three-dimensional, structural data which enabled the xylem networks to be described using graph theory. Using an array of network metrics as multidimensional descriptors, we compared the xylem networks between species and showed relationships to simulated and experimental measures of drought resistance. In addition to providing insight on drought resistance, these approaches offer new ways for comparative analysis of networks applicable to many systems.
Ancient DNA confirms anaemia as the cause for Porotic Hyperostosis in ancient Neolithics together with a genetic architecture for low bone mineral density
Authors: Ferrando-Bernal Manuel
Published: January 2023

Porotic hyperostosis is a disease that used to have an important prevalence during the Neolithic. Several hypotheses have been described to explain its origin but not one has been tested genetically. Here, I used hundreds of SNPs to confirm anaemia and low bone mineral density as the main cause for this disease using data for 80 ancient individuals for which it is known if they had or not the disease. Additionally, Neolithic individuals show the lowest bone mineral density and haemoglobin levels of all other periods tested here, explaining the highest prevalence of the porotic hyperostosis during this age.