bluuebunny/crossref_metadata_2025 huggingface dataset:
Hysteria, head injuries and heredity: ‘shell-shocked’ soldiers of the Royal Edinburgh Asylum, Edinburgh (1914–24)
Authors: Park Joanna , Neilson Louise , Demetriades Andreas K.
Published: March 2022

This project illustrates as-yet-uncharted psychiatric patients from the Royal Edinburgh Asylum (REA) around the time of World War I, predominantly ‘shell-shocked’ soldiers. Primary patient notes help to elucidate definitions, symptoms and perceptions of ‘shell-shock’, in addition to its links with other psychiatric conditions. This includes general paralysis of the insane (GPI), alcohol excess, mania and melancholia. Whereas the majority of these patients were suffering from shell-shock, it is not once explicitly listed as a diagnosis; it was a term whose use was discouraged by the War Office and key medical experts from 1916 onwards. As such, this paper demonstrates effects that canonical views held by the War Office and military psychiatrists on shell-shock aetiology had on language used in psychiatric patient notes. The results corroborate wartime views that mental distress due to a physical head injury was preferable to shell-shock without obvious cause; that neurasthenia was a more desirable diagnostic label than hysteria; and that mental illness was predominantly due to an inherited flaw in someone's character. Language used by psychiatrists to describe their patients was influenced by contemporary perspectives on gender, class and mental illness. More broadly, this paper adds to discussions about definitions and symptomatology of shell-shock that are being uncovered in historical patient notes from this period.
Crystals of TELSAM–target protein fusions that exhibit minimal crystal contacts and lack direct inter-TELSAM contacts
Authors: Nawarathnage Supeshala , Soleimani Sara , Mathis Moriah H. , Bezzant Braydan D. , Ramírez Diana T. , Gajjar Parag , Bunn Derick R. , Stewart Cameron , Smith Tobin , Pedroza Romo Maria J. , Brown Seth , Doukov Tzanko , Moody James D.
Published: March 2022

While conducting pilot studies into the usefulness of fusion to TELSAM polymers as a potential protein crystallization strategy, we observed novel properties in crystals of two TELSAM–target protein fusions, as follows. (i) A TELSAM–target protein fusion can crystallize more rapidly and with greater propensity than the same target protein alone. (ii) TELSAM–target protein fusions can be crystallized at low protein concentrations. This unprecedented observation suggests a route to crystallize proteins that can only be produced in microgram amounts. (iii) The TELSAM polymers themselves need not directly contact one another in the crystal lattice in order to form well-diffracting crystals. This novel observation is important because it suggests that TELSAM may be able to crystallize target proteins too large to allow direct inter-polymer contacts. (iv) Flexible TELSAM–target protein linkers can allow target proteins to find productive binding modes against the TELSAM polymer. (v) TELSAM polymers can adjust their helical rise to allow fused target proteins to make productive crystal contacts. (vi). Fusion to TELSAM polymers can stabilize weak inter-target protein crystal contacts. We report features of these TELSAM–target protein crystal structures and outline future work needed to validate TELSAM as a crystallization chaperone and determine best practices for its use.
Helicoverpa armigera
miR-2055 regulates lipid metabolism via fatty acid synthase expression
Authors: Cheng Yang , Lu Tengfei , Guo Junliang , Lin Zhe , Jin Qiao , Zhang Xiaoming , Zou Zhen
Published: March 2022

Insect hormones and microRNAs regulate lipid metabolism, but the mechanisms are not fully elucidated. Here, we found that cotton bollworm larvae feeding on
Arabidopsis thaliana
(AT) leaves had a lower triacylglycerol (TAG) level and more delayed development than individuals feeding on artificial diet (AD). Association analysis of small RNA and mRNA revealed that the level of miR-2055, a microRNA related to lipid metabolism, was significantly higher in larvae feeding on AT. Dual-luciferase reporter assays demonstrated miR-2055 binding to 3′ UTR of fatty acid synthase (FAS) mRNA to suppress its expression. Elevating the level of miR-2055 in larvae by agomir injection decreased FAS mRNA and protein levels, which resulted in reduction of free fatty acid (FFA) and TAG in fat body. Interestingly,
in vitro
assays illustrated that juvenile hormone (JH) increased miR-2055 accumulation in a dosage-dependent manner, whereas knockdown of Methoprene tolerant (Met) or Kruppel homologue 1 (Kr-h1) decreased the miR-2055 level. This implied that JH induces the expression of miR-2055 via a Met-Kr-h1 signal. These findings demonstrate that JH and miRNA cooperate to modulate lipid synthesis, which provides new insights into the regulatory mechanisms of metabolism in insects.
Harmonic-measure distribution functions for a class of multiply connected symmetrical slit domains
Authors: Green Christopher C. , Snipes Marie A. , Ward Lesley A. , Crowdy Darren G.
Published: March 2022

The harmonic-measure distribution function, or

h

-function, of a planar domain

Ω
⊂

C

with respect to a basepoint

z
0

∈
Ω

is a signature that profiles the behaviour in

Ω

of a Brownian particle starting from

z
0

. Explicit calculation of

h

-functions for a wide array of simply connected domains using conformal mapping techniques has allowed many rich connections to be made between the geometry of the domain and the behaviour of its

h

-function. Until now, almost all

h

-function computations have been confined to simply connected domains. In this work, we apply the theory of the Schottky–Klein prime function to explicitly compute the

h

-function of the doubly connected slit domain

C

∖

(
[
−
1

/

2
,
−
1

/

6
]
∪
[
1

/

6
,
1

/

2
]
)

. In view of the connection between the middle-thirds Cantor set and highly multiply connected symmetric slit domains, we then extend our methodology to explicitly construct the

h

-functions associated with symmetric slit domains of arbitrary even connectivity. To highlight both the versatility and generality of our results, we graph the

h

-functions associated with quadruply and octuply connected slit domains.
‘Inert’ ingredients are understudied, potentially dangerous to bees and deserve more research attention
Authors: Straw Edward A. , Thompson Linzi J. , Leadbeater Ellouise , Brown Mark J. F.
Published: March 2022

Agrochemical formulations are composed of two broad groups of chemicals: active ingredients, which confer pest control action, and ‘inert’ ingredients, which facilitate the action of the active ingredient. Most research into the effects of agrochemicals focusses on the effects of active ingredients. This reflects the assumption that ‘inert’ ingredients are non-toxic. A review of relevant research shows that for bees, this assumption is without empirical foundation. After conducting a systematic literature search, we found just 19 studies that tested the effects of ‘inert’ ingredients on bee health. In these studies, ‘inert’ ingredients were found to cause mortality in bees through multiple exposure routes, act synergistically with other stressors and cause colony level effects. This lack of research is compounded by a lack of diversity in study organism used. We argue that ‘inert’ ingredients have distinct, and poorly understood, ecological persistency profiles and toxicities, making research into their individual effects necessary. We highlight the lack of mitigation in place to protect bees from ‘inert’ ingredients and argue that research efforts should be redistributed to address the knowledge gap identified here. If so-called ‘inert’ ingredients are, in fact, detrimental to bee health, their potential role in widespread bee declines needs urgent assessment.
Downtown diet: a global meta-analysis of increased urbanization on the diets of vertebrate predators
Authors: Gámez Siria , Potts Abigail , Mills Kirby L. , Allen Aurelia A. , Holman Allyson , Randon Peggy M. , Linson Olivia , Harris Nyeema C.
Published: March 2022

Predation is a fundamental ecological process that shapes communities and drives evolutionary dynamics. As the world rapidly urbanizes, it is critical to understand how human perturbations alter predation and meat consumption across taxa. We conducted a meta-analysis to quantify the effects of urban environments on three components of trophic ecology in predators: dietary species richness, dietary evenness and stable isotopic ratios (IRs) (δ13C andδ15N IR). We evaluated whether the intensity of anthropogenic pressure, using the human footprint index (HFI), explained variation in effect sizes of dietary attributes using a meta-regression. We calculated Hedges’geffect sizes from 44 studies including 11 986 samples across 40 predatory species in 39 cities globally. The direction and magnitude of effect sizes varied among predator taxa with reptilian diets exhibiting the most sensitivity to urbanization. Effect sizes revealed that predators in cities had comparable diet richness, evenness and nitrogen ratios, though carbon IRs were more enriched in cities. We found that neither the 1993 nor 2009 HFI editions explained effect size variation. Our study provides, to our knowledge, the first assessment of how urbanization has perturbed predator–prey interactions for multiple taxa at a global scale. We conclude that the functional role of predators is conserved in cities and urbanization does not inherently relax predation, despite diets broadening to include anthropogenic food sources such as sugar, wheat and corn.
Emerging infectious disease triggered a trophic cascade and enhanced recruitment of a masting tree
Authors: Bogdziewicz Michał , Kuijper Dries , Zwolak Rafał , Churski Marcin , Jędrzejewska Bogumiła , Wysocka-Fijorek Emilia , Gazda Anna , Miścicki Stanisław , Podgórski Tomasz
Published: March 2022

There are several mechanisms that allow plants to temporarily escape from top-down control. One of them is trophic cascades triggered by top predators or pathogens. Another is satiation of consumers by mast seeding. These two mechanisms have traditionally been studied in separation. However, their combined action may have a greater effect on plant release than either process alone. In 2015, an outbreak of a disease (African swine fever, ASF) caused a crash in wild boar (
Sus scrofa
) abundance in Białowieża Primeval Forest. Wild boar are important consumers of acorns and are difficult to satiate relative to less mobile granivores. We hypothesized that the joint action of the ASF outbreak and masting would enhance regeneration of oaks (
Quercus robur
). Data from ungulate exclosures demonstrated that ASF led to reduction in acorn predation. Tree seedling data indicated that oak recruitment increased twofold relative to pre-epidemic period. Our results showed that perturbations caused by wildlife disease travel through food webs and influence forest dynamics. The outbreak of ASF acted synergistically with masting and removed herbivore top-down control of oaks by mobile consumers. This illustrates that the ASF epidemic that currently occurs across Europe can have broad effects on forest dynamics.
Experimental demonstration of prenatal programming of mitochondrial aerobic metabolism lasting until adulthood
Authors: Stier Antoine , Monaghan Pat , Metcalfe Neil B.
Published: March 2022

It is increasingly being postulated that among-individual variation in mitochondrial function underlies variation in individual performance (e.g. growth rate) and state of health. It has been suggested (but not adequately tested) that environmental conditions experienced before birth could programme postnatal mitochondrial function, with persistent effects potentially lasting into adulthood. We tested this hypothesis in an avian model by experimentally manipulating prenatal conditions (incubation temperature and stability) and then measuring mitochondrial aerobic metabolism in blood cells from the same individuals during the middle of the growth period and at adulthood. Mitochondrial aerobic metabolism changed markedly across life stages, and parts of these age-related changes were influenced by the prenatal temperature conditions. A high incubation temperature induced a consistent and long-lasting increase in mitochondrial aerobic metabolism. Postnatal mitochondrial aerobic metabolism was positively associated with oxidative damage on DNA but not telomere length. While we detected significant within-individual consistency in mitochondrial aerobic metabolism across life stages, the prenatal temperature regime only accounted for a relatively small proportion (less than 20%) of the consistent among-individual differences we observed. Our results demonstrate that prenatal conditions can programme consistent and long-lasting differences in mitochondrial function, which could potentially underlie among-individual variation in performance and health state.
Evaluation of Postgraduate Educational Environment of Doctors Training in Psychiatry: a mixed method study
Authors: Elzain Musaab , Moran Lisa , McCarthy Geraldine , Hyde Sarah , McFarland John
Published: March 2022

Introduction

Educational Environment (EE) is of paramount importance in Medical Education, but can be intangible and hard to clearly determine. Professional satisfaction and patient care improve in a pleasant learning environment; where postgraduate physicians are encouraged, suitably supervised, and fostered. A negative learning environment can be detrimental to trainees’ and teams’ morale and can jeopardize the multidisciplinary working relationship.

Objectives

The objective of this study was to measure the Educational Environment (EE) of Psychiatry postgraduate training in the Midwest of Ireland training Deanery; what aspects of training are working well and what areas are seen as not optimal.

Methods

This study took place between April and June 2021. A mixed methods approach was adopted, using the Postgraduate Hospital Educational Environment Measure (PHEEM) and semi-structured one-to-one interviews.

Results

Response rate was 88% (n=22). The total PHEEM score was 105.64±23.52, indicating a postgraduate EE with more positive than negative aspects, but with room for improvement. There were no differences in overall PHEEM and subscale scores between trainees’ gender, training grades or years of working experience. Three themes were identified that contribute to trainees’ perception of EE: the commitment of the trainees’ supervisors to the role they play in trainees’ overall development, the clinical workload of the trainee, and the day-to-day working conditions of the trainee. Definite disparities between work placements were evident in the collected data across these three themes.

Conclusions

Although the training program had an overall positive EE, specific answers and interview themes indicated some areas of weakness that may contribute to trainee dissatisfaction and possible burnout. Planned interventions targeting these areas and tracking changes in EE and burnout rates over time may be useful measures going forward.

Declaration of Interest

None
Rapid review of government issued documents relevant to mitigation of COVID-19 in the US food manufacturing and processing industry
Authors: Chen Ziqian , Bulut Ece , Trmčić Aljoša , Ivanek Renata
Published: March 2022

We surveyed publicly available records published by the United States (US) government between the start of the Coronavirus Disease 2019 (COVID-19) pandemic and September 30th, 2021, to identify documents containing resources or guidelines about COVID-19 mitigation relevant to the US food manufacturing and processing industry (hereafter referred to as “the food processing industry”). Among 36 documents identified and reviewed (including 35 from government agencies and one from a relevant professional association), we extracted 19 categories of mitigation strategies covering the themes of employee biosafety, surveillance, vaccination, social distancing, and worker education. We concluded that the priority of COVID-19 mitigation in the food processing industry was to protect the health and safety of industry workers while maintaining food supply chain resilience to minimize disturbance in the food market and avoid food crisis. A collated list of the identified documents and their comprehensive review will (i) aid researchers and public health workers in interpreting the potential impacts of the recommended mitigations on the epidemiology of the disease among workers in the food processing industry and (ii) help the food processing industry sort out the most essential strategies to take in face of a pandemic.
Macrophage depletion blocks congenital SARM1-dependent neuropathy
Authors: Dingwall Caitlin B. , Strickland Amy , Yum Sabrina W. , Yim Aldrin K. , Zhu Jian , Wang Peter L. , Yamada Yurie , Schmidt Robert E. , Sasaki Yo , Bloom A. Joseph , DiAntonio Aaron , Milbrandt Jeffrey
Published: March 2022

Axon loss contributes to many common neurodegenerative disorders. In healthy axons, the axon survival factor NMNAT2 inhibits SARM1, the central executioner of programmed axon degeneration. We identified two rare NMNAT2 missense variants in two brothers afflicted with a progressive neuropathy syndrome. The polymorphisms result in amino acid substitutions, V98M and R232Q, which reduce NMNAT2 NAD+-synthetase activity. We generated a mouse model of the human syndrome and found that Nmnat2V98M/Nmnat2R232Q compound-heterozygous CRISPR mice survive to adulthood but develop progressive motor dysfunction, peripheral axon loss, and macrophage infiltration. These disease phenotypes are all SARM1-dependent. Remarkably, macrophage depletion therapy blocks and reverses neuropathic phenotypes in Nmnat2V98M/R232Q mice, identifying a SARM1-dependent neuroimmune mechanism as a key driver of disease pathogenesis. These findings demonstrate that SARM1 induces an inflammatory neuropathy and highlight the potential of immune therapy to treat this rare syndrome and other neurodegenerative conditions associated with NMNAT2 loss and SARM1 activation.
CLE42 Delays Leaf Senescence by Antagonizing Ethylene Pathway in Arabidopsis
Authors: Zhang Yi , Tan Shuya , Gao Yuhan , Kan Chengcheng , Wang Hou-Ling , Yang Qi , Xia Xinli , Ishida Takashi , Sawa Shinichiro , Guo Hongwei , Li Zhonghai
Published: March 2022

Leaf senescence is the final stage of leaf development and is influenced by numerous internal and environmental factors. CLE family peptides are plant-specific peptide hormones that regulate various developmental processes. However, the role of CLE in regulating leaf senescence remains unclear. Here, we found that CLE42 is a negative regulator of leaf senescence by using a CRISPR/Cas9-produced CLE mutant collection. The cle42 mutant displayed earlier senescence phenotypes, while overexpression of CLE42 delayed age-dependent and dark-induced leaf senescence. Moreover, application of the synthesized 12-aa peptide (CLE42p) also delayed leaf senescence under natural and dark conditions. CLE42 and CLE41/44 displayed functional redundancy in leaf senescence, and the cle41 cle42 cle44 triple mutant displayed more pronounced earlier senescence phenotypes than any single mutant. Analysis of differentially expressed genes obtained by RNA-Seq methodology revealed that ethylene pathway was suppressed by overexpressing CLE42. Moreover, CLE42 suppressed ethylene biosynthesis and thus promoted the protein accumulation of EBF, which in turn decreased the function of EIN3. Accordingly, mutation of EIN3/EIL1 or overexpression of EBF1 suppressed the earlier senescence phenotypes of the cle42 mutant. Together, our results reveal that the CLE peptide hormone regulates leaf senescence by communicating with ethylene pathway.
Fine-mapping and identification of candidate causal genes for tail length in the Merinolandschaf breed
Authors: Lagler Dominik Karl , Hannemann Elisabeth , Eck Kim , Klawatsch Jürgen , Seichter Doris , Russ Ingolf , Mendel Christian , Lühken Gesine , Krebs Stefan , Blum Helmut , Upadhyay Maulik , Međugorac Ivica
Published: March 2022

Background

Docking the tails of young lambs in long-tailed sheep breeds is a common practice worldwide. This practice is associated with pain, suffering and damage to the affected animals. Breeding for a shorter tail in long-tailed sheep breeds could offer one of the alternatives. This study aimed to analyze the natural tail length variation in the most common German Merino variety, and to identify possible causal alleles for the short tail phenotype segregating within a typical long-tailed breed.

Results

Haplotype-based mapping in 362 genotyped (Illumina OvineSNP50) and phenotyped Merinolandschaf lambs resulted in a genome-wide significant mapping at position 37,111,462 bp on sheep chromosome 11 and on chromosome 2 at position 94,538,115 bp (Oar_v4.0). Targeted capture sequencing of these regions in 48 selected sheep and comparative analyses of WGS data of various long and short-tailed sheep breeds as well as wild sheep subspecies identified a SNP and a SINE element as the promising candidates. The PCR genotyping of these candidates revealed complete linkage of both the candidate variants. The SINE element is located in the promotor region of HOXB13, while the SNP was located in the first exon of HOXB13 and predicted to result in a nonsynonymous mutation.

Conclusions

Our approach successfully identified HOXB13 as candidate genes and the likely causal variants for tail length segregating within a typical long-tailed Merino breed. This would enable more precise breeding towards shorter tails, improve animal welfare by amplification of ancestral alleles and contribute to a better understanding of differential embryonic development.
Social cues of safety can override differences in threat level
Authors: Ferreira Clara H , Heinemans Mirjam , Farias Matheus , Gonçalves Rui , Moita Marta A
Published: March 2022

Animals in groups integrate social information with that directly-gathered about the environment to guide decisions regarding reproduction, foraging and defense against predatory threats. In the context of predation, usage of social information has acute fitness benefits, aiding the detection of predators, the mounting of concerted defensive responses, or allowing the inference of safety, permitting other beneficial behaviors such as foraging for food. Individual and group defense responses to predatory threats can vary in modality and vigor depending on the perceived threat level. Moreover, predation level has been shown to modulate the use of social cues about foraging sites. Whether and how different threat levels affect the use of social cues to guide defense responses, is currently unknown. We previously showed that Drosophila melanogaster display a graded decrease in freezing behavior, triggered by an inescapable visual threat, with increasing group sizes. Crucially, we identified the movement of others as a cue of safety and its cessation a cue of threat and found the group responses to be primarily guided by the safety cues, resulting in a net social buffering effect. Here, we investigated how threat level impacts the use of social cues by exposing flies individually and in groups to two threat imminences using looms of different speeds. We show that freezing responses are stronger to the faster looms regardless of social condition. However, social buffering was stronger for groups exposed to the fast looms, such that the increase in freezing caused by the higher threat was less prominent in flies tested in groups than those tested individually. Through artificial control of behavior, we created different group compositions, titrating the motion cues that were maintained across threat levels. We, found that the same level of safety motion cues had a bigger weight on the flies’ decisions when these were exposed to the higher threat, thus overriding differences in perceived threat levels. These findings shed light on the ‘safety in numbers’ effect, revealing the modulation of the saliency of social safety cues across threat intensities, a possible mechanism to regulate costly defensive responses.
Reconstructing the evolutionary history of a B cell lineage with minimum spanning tree and genotype abundances
Authors: Abdollahi Nika , Jeusset Lucile , de Septenville Anne , Davi Frédéric , Bernardes Juliana S.
Published: March 2022

B cell receptor (BCR) genes exposed to an antigen undergo somatic hypermutations and Darwinian antigen selection, generating a large BCR-antibody diversity. This process, known as B cell affinity maturation, increases antibody affinity, forming a specific B cell lineage that includes the unmutated ancestor and mutated variants. In a B cell lineage, cells with a higher antigen affinity will undergo clonal expansion, while those with a lower affinity will not proliferate and probably be eliminated. Therefore, cellular (genotype) abundance provides a valuable perspective on the ongoing evolutionary process. Phylogenetic tree inference is often used to reconstruct B cell lineage trees and represents the evolutionary dynamic of BCR affinity maturation. However, such methods should process B cell population data derived from experimental sampling that might contain different cellular abundances. There are a few phylogenetic methods for reconstructing the evolutionary history of B cell lineages; best-performing solutions are time-demanding and restricted to analyzing a reduced number of BCR IGH sequences, while time-efficient methods do not consider cellular abundances. We propose ClonalTree, a low-complexity and accurate approach to reconstruct B cell lineage trees that incorporates genotype abundances into minimum spanning tree (MST) algorithms. Using both simulated and experimental data, we demonstrated that ClonalTree outperforms MST-based algorithms and achieves a similar performance compared to a method that explores tree generating space exhaustively. However, ClonalTree has a lower running time, being more convenient for reconstructing phylogenetic lineage trees from high-throughput BCR sequencing data, mainly in biomedical applications, where a lower computational time is appreciable. It is hundreds to thousands of times faster than exhaustive approaches, enabling the analysis of a large set of sequences within minutes or seconds and without loss of accuracy. The source code is freely available at github.com/julibinho/ClonalTree.
Stable nebulization and muco-trapping properties of Regdanvimab/IN-006 supports its development as a potent, dose-saving inhaled therapy for COVID-19
Authors: McSweeney Morgan , Stewart Ian , Richardson Zach , Kang Hyunah , Park Yoona , Kim Cheolmin , Tiruthani Karthik , Wolf Whitney , Schaefer Alison , Kumar Priya , Aurora Harendra , Hutchins Jeff , Cho Jong Moon , Hickey Anthony J. , Lee Soo Young , Lai Samuel
Published: March 2022

The respiratory tract represents the key target for antiviral delivery in early interventions to prevent severe COVID-19. While neutralizing monoclonal antibodies (mAb) possess considerable efficacy, their current reliance on parenteral dosing necessitates very large doses and places a substantial burden on the healthcare system. In contrast, direct inhaled delivery of mAb therapeutics offers the convenience of self-dosing at home, as well as much more efficient mAb delivery to the respiratory tract. Here, building on our previous discovery of Fc-mucin interactions crosslinking viruses to mucins, we showed that regdanvimab, a potent neutralizing mAb already approved for COVID-19 in several countries around the world, can effectively trap SARS-CoV-2 virus-like-particles in fresh human airway mucus. IN-006, a reformulation of Regdanvimab, was stably nebulized across a wide range of concentrations, with no loss of activity and no formation of aggregates. Finally, nebulized delivery of IN-006 resulted in 100-fold greater mAb levels in the lungs of rats compared to serum, in marked contrast to intravenously dosed mAbs. These results not only support our current efforts to evaluate the safety and efficacy of IN-006 in clinical trials, but more broadly substantiate nebulized delivery of human antiviral mAbs as a new paradigm in treating SARS-CoV-2 and other respiratory pathologies.
Increased reliability of visually-evoked activity in area V1 of the MECP2-duplication mouse model of autism
Authors: Ash Ryan T. , Palagina Ganna , Park Jiyoung , Fernandez-Leon Jose A. , Seilheimer Rob , Lee Sangkyun , Sabharwal Jasdeep , Reyes Fredy , Wang Jing , Lu Dylan , Wu Sam , Smirnakis Stelios M.
Published: March 2022

Atypical sensory processing is now thought to be a core feature of the autism spectrum. Influential theories have proposed that both increased and decreased neural response reliability within sensory systems could underlie altered sensory processing in autism. Here, we report evidence for abnormally increased reliability of visual-evoked responses in layer 2/3 neurons of adult primary visual cortex in the MECP2-duplication syndrome animal model of autism. Increased response reliability was due in part to decreased response amplitude, decreased fluctuations in endogenous activity, and decreased neuronal coupling to endogenous activity. Similarly to what was observed neuronally, the optokinetic reflex occurred more reliably at low contrasts in mutant mice compared to controls. Retinal responses did not explain our observations. These data suggest that the circuit mechanisms for convolution of sensory-evoked and endogenous signal and noise may be altered in this form of syndromic autism.
Rational evolution of a recombinant DNA polymerase for efficient incorporation of unnatural nucleotides by dual-site boosting
Authors: Cao Ruyin , Zhai Lili , Xie Qingqing , Wang Zi , Zheng Yue , Zhang Wenwei , Bull Alexander Kai , Xu Xun , Dong Yuliang , Xu Chongjun , Lyu Wenping
Published: March 2022

Machine learning modelling assisting function-oriented enzyme engineering is normally built on predefined protein sequence space. However, efficient defining the determinant amino acid positions upon which the combinatorial mutation library is constructed is still a challenge in protein science. Herein, we present a comprehensive investigation of modifying a recombinant DNA polymerase for efficient incorporating one unnatural nucleotide, including the identification of key sites/regions, machine learning-assisted mutants screening, and the underlying mechanism of kinetics boosting. By using hundreds of training points and only dozens of testing samples, we found that one highly engineered enzyme’s catalytic efficiency can be further improved by one order of magnitude by specific mutation on two sites, 485I and 451L. Compared to the position 485 which is known to dominate local conformation of B-family DNA polymerases, 451 is a split-new active site discovered by our approach. A novel allosteric regulation mechanism is underlying the apparent synergy of 485I and 451L on the kinetics boosting. As a result, a “half-closed” conformation of the binding pocket and a cooperative binding of both primer and template DNA strands on the protein accelerated the processes of substrate’s incorporation, molecular recognition, and releasing of incorrect nucleotides. These findings have implications in guiding the function-tuning of DNA polymerases for a broad range of biotechnological applications.
More persistent bacterial than fungal associations in the microbiota of a pest
Authors: Gurung Kiran , Vink Stefanie Nicoline , Salles Joana Falcão , Wertheim Bregje
Published: March 2022

The invasive fly Drosophila suzukii is a pest that can infest a diverse range of intact, ripening fruits, using its serrated ovipositor. This constitutes a different niche compared to the rotting fruits its ancestors use, especially because these intact fruits have limited quantities of microbes and soluble nutrients for the developing larvae. To investigate the potential role of microbial associations in the niche expansion of this invasive fly, we characterized the bacterial and fungal communities of D. suzukii and various wild fruits from which they developed. To assess cross-generational microbial associations, we also lab-reared fly populations and characterized their microbial communities. Diversity metrics of microbial communities differed significantly between flies and fruits. Different fruit types varied substantially in microbial composition, while flies showed relatively uniform bacterial communities, irrespective of the fruit source they developed on. After lab-rearing, bacterial communities still showed considerable overlap with those of wild flies. Fungal communities of flies and fruits showed larger resemblance, with a substantial overlap between wild flies and the corresponding fruits on which they had developed. Our study thus reports that the fungal community structure in these pests largely reflects those on the breeding substrates, while these flies might have formed more persistent associations with bacteria and transmit these across generations rather than obtaining them from their food source.
Combinatorial engineering for photoautotrophic production of recombinant products from the green microalga Chlamydomonas reinhardtii
Authors: Abdallah Malak N. , Wellman Gordon B. , Overmans Sebastian , Lauersen Kyle J.
Published: March 2022

Chlamydomonas reinhardtii has emerged as a powerful green cell factory for metabolic engineering of sustainable products created from the photosynthetic lifestyle of this microalga. Advances in nuclear genome and transgene expression engineering are allowing robust engineering strategies to be demonstrated in this host. However, commonly used lab strains are not equipped with features to enable their broader implementation in non-sterile conditions and high-cell density concepts. Here, we use combinatorial chloroplast and nuclear genome engineering to complement the C. reinhardtii strain UVM4 with publicly available genetic tools to enable the use of inorganic phosphite and nitrate as a sole the source phosphorous and nitrogen, respectively. We present recipes to create phosphite-buffered media solutions that enable high cell density algal cultivation. We then combine previously reported engineering strategies to produce the heterologous sesquiterpenoid patchoulol to high titers from our engineered green cell factories and show these products are possible to produce in under non-sterile conditions. Our work presents a straightforward means to generate C. reinhardtii strains for broader application in bio-processes for the sustainable generation of products.
In Silico Evaluation of Plant Nitrification Suppression Effects on Agroecosystem Nitrogen Loss
Authors: Hartman Melannie D. , Burnham Mark , Parton William J. , Finzi Adrien , DeLucia Evan , Yang Wendy H.
Published: March 2022

Abstract

Nitrification regulates potential for nitrogen (N) loss from ecosystems because it converts ammonium to nitrate, which is susceptible to leaching and gaseous emissions. Crops can suppress the microbes that perform nitrification by exuding nitrification-inhibiting compounds from their roots and taking up available ammonium, the substrate for nitrification. However, the effect of nitrification suppression on agroecosystem N losses remains poorly characterized, and a lack of temporal synchrony between nitrification, N losses, and nitrification suppression by plants could limit the effect of nitrification suppression. We used the DayCent-CABBI model to evaluate the effectiveness of the suppression of nitrification by sorghum to reduce N2O emissions and nitrate leaching in an energy sorghum/soybean rotation at the Energy Farm in Urbana-Champaign, IL. We simulated nitrification suppression at the measured levels (measNS) and at the maximum measured level applied to the entire growing season (maxNS), and we also explored ways to better utilize nitrification suppression by altering the timing of UAN fertilizer applications. Model experiments showed that most nitrification occurred immediately after fertilizer was applied, whereas nitrification suppression begins to ramp up more than a month after planting. On an annual basis, measNS experiments showed a 1-2% reduction in annual N2O emissions relative to no nitrification suppression (noNS), and maxNS experiments showed a 4-9% reduction in annual N2O emissions relative to noNS. Both nitrification suppression levels showed < 1% reduction in nitrate leaching. Altering the timing of fertilizer applications to better synchronize nitrification suppression with high soil ammonium levels had mixed effects on annual N2O emissions and nitrate leaching and sometimes resulted in increased N losses. The timing of simulated N2O emissions shifted with the timing of fertilization, and N2O emissions from denitrification increased when N2O emissions from nitrification decreased. Increasing N retention during the non-growing season may be more effective and growing-season nitrification suppression for reducing annual N losses in the rainfed Midwest, particularly for NO3- leaching in the early spring. Optimizing the timing of nitrification suppression alongside off-season N retention strategies would best improve the N sustainability of agroecosystems.
Social deficits induced by pervasive environmental stressors are prevented by microbial or dopaminergic modulation
Authors: Smith Caroline J. , Rendina Danielle N. , Kingsbury Marcy A. , Malacon Karen E. , Nguyen Dang M. , Tran Jessica J. , Devlin Benjamin A. , Clark Madeline J. , Raju Ravikiran M. , Burgett Lauren , Zhang Jason H. , Cetinbas Murat , Sadreyev Ruslan I. , Chen Kevin , Iyer Malvika S. , Bilbo Staci D.
Published: March 2022

Environmental toxicant exposure, including air pollution, is increasing worldwide. However, toxicant exposures are not equitably distributed. Rather, low-income and minority communities bear the greatest burden, along with higher levels of psychosocial stress. Both air pollution and maternal stress during pregnancy have been linked to neurodevelopmental disorders such as autism, but biological mechanisms and targets for therapeutic intervention remain poorly understood. We demonstrate that combined prenatal exposure to air pollution (diesel exhaust particles, DEP) and maternal stress (MS) in mice induces social behavior deficits only in male offspring, in line with the male bias in autism. These behavioral deficits are accompanied by changes in microglia and dopaminergic circuits in the brain, along with changes in the structure of the gut epithelium and microbiome. Importantly, DEP/MS-induced social deficits in males are prevented by shifting the gut microbiome by cross-fostering at birth and reversed by chemogenetic activation of the dopamine system.
Identification of different classes of genome instability suppressor genes through analysis of DNA damage response markers
Authors: Li Bin-Zhong , Kolodner Richard D. , Putnam Christopher D.
Published: March 2022

Genetic studies inSaccharomyces cerevisiaehave identified 266 genes and predicted an additional 38 genes that suppress the accumulation of spontaneous gross chromosomal rearrangements (GCRs). Here we identified mutations that induce two DNA damage response (DDR) markers, Hug1 expression and Ddc2 foci, and combined these data with other published screens identifying mutations inducing other DDR markers, including Rad52 foci and Rnr3 expression. Together, these data identify four categories of mutations: most mutations were DDR- GCR-, 356 were DDR+ GCR-, 72 were DDR- GCR+, and 157 were DDR+ GCR+. These results indicate that induction of DDR markers alone, while allowing DDR analysis, is not a reliable indicator of increased genome instability. They also guide further analysis of mechanistically distinct groups of GCR-inducing mutations, such as mutations that increase levels of GCR-inducing DNA damage and mutations that result in mis-repair of normal levels of DNA damage resulting in GCRs.
Realtime morphological characterization and sorting of unlabeled viable cells using deep learning
Authors: Salek Mahyar , Li Nianzhen , Chou Hou-Pu , Saini Kiran , Jovic Andreja , Jacobs Kevin B. , Johnson Chassidy , Lee Esther J. , Chang Christina , Nguyen Phuc , Mei Jeanette , Pant Krishna P. , Wong-Thai Amy Y. , Smith Quillan F. , Huang Stephanie , Chow Ryan , Cruz Janifer , Walker Jeff , Chan Bryan , Musci Thomas J. , Ashley Euan A. , Masaeli Maddison (Mahdokht)
Published: March 2022

Phenotyping of single cells has dramatically lagged advances in molecular characterization and remains a manual, subjective, and destructive process. We introduce COSMOS, a platform for phenotyping and enrichment of cells based on deep learning interpretation of high-content morphology data in realtime. By training models on an atlas of >1.5 billion images, we demonstrate enrichment of unlabeled cells up to 33,000 fold. We apply COSMOS to multicellular tissue biopsy samples demonstrating that it can identify malignant cells with similar accuracy to molecular approaches while enriching viable cells for functional evaluation. We show high-dimensional embedding vectors of morphology generated by COSMOS without any need for complex sample pre-processing, gating, or bioinformatics capabilities, which enables discovery of cellular phenotypes, and integration of morphology into multi-dimensional analyses.

One sentence summary

A novel platform capable of high-throughput imaging and gently sorting cells using deep morphological assessment.
Longitudinal monitoring of SARS-CoV-2 neutralizing antibody titers and its impact on employee personal wellness decisions
Authors: Vandergaast Rianna , Carey Timothy , Suksanpaisan Lukkana , Lathrum Chase , Narjari Riya , Haselton Michelle , Schnebeck Luke , Wijesekara Aroshi , Duncan Andrew , Russell Luke , Naik Shruthi , Peng Kah-Whye , Lech Patrycja , Russell Stephen J.
Published: March 2022

Virus neutralizing antibody (vnAb) titers are the strongest laboratory correlate of protection from SARS-CoV-2. Providing individuals with real-time measures of their vnAb titers is predicted to improve their ability to make personal wellness decisions. Yet, widespread commercial testing of SARS-CoV-2 vnAbs does not currently occur. Here, we examined whether knowing their vnAb titer impacted wellness decision-making among individuals. To this end, starting on January 1, 2021, we offered all employees from two companies free IMMUNO-COV™ testing and conducted a survey to assess their behaviors and decisions regarding booster vaccination. IMMUNO-COV is a clinically validated, surrogate virus assay that quantitates serum titers of SARS-CoV-2 vnAbs. To help participants gauge their level of protection based on their vnAb titer, we calibrated IMMUNO-COV titers to the World Health Organization (WHO) International Standard (IU/mL), making them comparable to published reports of correlates of protection, and we fit historical IMMUNO-COV vnAb titer values into predictive models of immune protection from COVID-19. As expected, data for the 56 program participants showed variability in vnAb titers post vaccination, rates vnAb decay, and fold-increases in vnAb titers after booster vaccination. Based on the participant survey, the majority (66%) of participants indicated that knowing their vnAb titer impacted their social behaviors and/or their decision on the timing of a booster vaccination. Several participants indicated that knowing their vnAb titer contributed to their peace of mind regarding their high level of protection from COVID-19. Together, these data demonstrate that regular determination of SARS-CoV-2 neutralizing antibody titers can significantly impact decisions regarding social interactions and timing of booster vaccinations.
Understanding multimorbidity trajectories in Scotland: an application of sequence analysis
Authors: Cezard G. , Sullivan F. , Keenan K.
Published: March 2022

BACKGROUND

Although understanding how multiple conditions develop over time is of growing interest, there is currently little methodological development on the topic, especially in understanding how multimorbidity (the co-existence of at least two chronic conditions) develops longitudinally and in which order diseases occur. Therefore, we aim to describe how a longitudinal method, sequence analysis, can be used to understand the sequencing of common chronic diseases that lead to multimorbidity and the socio-demographic factors and health outcomes associated with typical disease trajectories.

METHODS

We use the Scottish Longitudinal Study (SLS) linking the Scottish census 2001 to disease registries, hospitalisation and mortality records. SLS participants aged 40-74 years at baseline were followed over a 10-year period (2001-2011) for the onset of three commonly occurring diseases: diabetes, cardiovascular disease (CVD), and cancer. We focused on participants who transitioned to at least two of these conditions over the follow-up period (N=6,300). We use sequence analysis with optimal matching and hierarchical cluster analysis to understand the process of disease sequencing and to distinguish typical multimorbidity trajectories. Socio-demographic differences between specific disease trajectories were evaluated using multinomial logistic regression. Poisson and Cox regressions were used to assess differences in hospitalisation and mortality outcomes between typical trajectories.

RESULTS

Individuals who transitioned to multimorbidity over 10 years were more likely to be older and living in more deprived areas than the rest of the population. We found seven typical trajectories: later fast transition to multimorbidity, CVD start with slow transition to multimorbidity, cancer start with slow transition to multimorbidity, diabetes start with slow transition to multimorbidity, fast transition to both diabetes and CVD, fast transition to multimorbidity and death, fast transition to both cancer and CVD. Those who quickly transitioned to multimorbidity and death were the most vulnerable, typically older, less educated, and more likely to live in more deprived areas. They also experienced higher number of hospitalisations and overnight stays while still alive.

CONCLUSIONS

Sequence analysis can strengthen our understanding of typical disease trajectories when considering a few key diseases. This may have implications for more active clinical review of patients beginning quick transition trajectories.
Reconstitution of renal cyst formation in 3D culture reveals a role for AMOT and Yap1 in determining cyst size
Authors: Wells Clark D. , Lange Kevin , Thompson Abigail F. , Xu Wei Min , Clendenon Sherry G. , Underwood John S. , Harris Peter , Herbert Britney-Shea , Glazier James , Wandinger-Ness Angela , Bacallao Robert L.
Published: March 2022

Despite substantial progress in identifying and understanding causative mutations in autosomal dominant polycystic kidney disease (ADPKD), little is known about subsequent cellular events leading to cyst formation. In prior studies we reported that Cadherin 8, a type II Cadherin, expression is sufficient to induce cyst emergence from HK-2 cells grown as tubule arrays in collagen matrix (1). However, emergent cysts did not exhibit the luminal enlargement observed in ADPKD. In this communication, we reconstitute cyst emergence with consequent cyst lumen expansion in 3D culture by stable co-expression of Cadherin 8 in combination with a constitutively active mutant of YAP1, the key effector of the HIPPO pathway. Specifically, immortalized cells derived from ADPKD cyst epithelia formed cysts with substantially larger lumen sizes when transduced with YAP1-5SA. Conversely, expression of the YAP1 inhibitor, AMOTL1, in these cells resulted in their forming cysts with smaller lumens than control cells. Our data show that cyst formation results from a sequential two-step process consisting of cyst initiation and subsequent cyst expansion. Taken together, cyst initiation induced by Cadherin 8 expression is proposed to result from decreased cell-cell adhesion while cyst expansion is driven by increased Yap1 activity.