bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing
Authors: Liu Andrew W. , Villar-Briones Alejandro , Luscombe Nicholas M. , Plessy Charles
Published: January 2022

In order to automate the genome sequencing pipeline in our laboratory, we programmed a dual-arm anthropomorphic robot, the Robotic Biology Institute’s Maholo LabDroid, to perform organic solvent-based genomic DNA extraction from cell lysates. To the best of our knowledge, this is the first time that automation of phenol-chloroform extraction has been reported. We achieved routine extraction of high molecular weight genomic DNA (>100 kb) from diverse biological samples including algae cultured in sea water, bacteria, whole insects, and human cell lines. The results of pulse-field electrophoresis size analysis and the N50 sequencing metrics of reads obtained from Nanopore MinION runs verified the presence of intact DNA suitable for direct sequencing. We present the workflow that can be used to program similar robots and discuss the problems and solutions we encountered in developing the workflow. The protocol can be adapted to analogous methods such as RNA extraction, and there is ongoing work to incorporate further post-extraction steps such as library construction. This work shows the potential for automated robotic workflows to free molecular biological researchers from manual interventions in routine experimental work. A time-lapse movie of the entire automated run can be seen at http://doi.org/10.6084/m9.figshare.17097065
Genetic basis and adaptive implications of temperature-dependent and temperature-independent effects of drought on chickpea phenology
Authors: Li Yongle , Lake Lachlan , Chauhan Yashvir S. , Taylor Julian , Sadras Victor O.
Published: January 2022

Water deficit often hastens flowering of pulses partially because droughted plants are hotter. Separating temperature-independent and temperature-dependent effects of drought is important to understand, model and manipulate phenology genetically and agronomically.

We define a new trait, drought effect on phenology (DEP = difference in flowering time between irrigated and rainfed crops), and use FST genome scan to probe for genomic regions under selection for this trait. Genomic regions overlapping for early- and late-sown crops would associate with temperature-independent effects and non-overlapping genomic regions would associate with temperature-dependent effects.

Time to flowering shortened with increasing water stress quantified with carbon isotope composition. Genomic regions on chromosomes 4, 5, 7 and 8 were under selection for DEP. An overlapping region for early and late sowing on chromosome 8 revealed a temperature-independent effect with four candidate genes: BAM1, BAM2, HSL2 and ANT. The non-overlapping regions included six candidate genes: EMF1, EMF2, BRC1/TCP18, BZR1, NPGR1 and ERF1.

Modelling to assess DEP adaptive value showed it reduces the likelihood of drought and heat stress at the expense of cold risk. Accounting for DEP would improve phenology models to predict adaptation to future climates and breeding against the combined risks of drought, heat, and cold stress.

Highlight

Predictive and genetic models that overlook drought effects on phenology can return biased predictions of adaptation to future climates. Here we study the genetic causes and adaptive consequences of hastened flowering under drought.
Parameterization and Application of the General Amber Force Field to Model Fluro Substituted Furanose Moieties and Nucleosides
Authors: Escalante Diego E. , Aldrich Courtney C. , Ferguson David M.
Published: January 2022

Molecular mechanics force field calculations have historically shown significant limitations in modeling the energetic and conformational interconversions of highly substituted furanose rings. This is primarily due to the gauche effect that is not easily captured using pairwise energy potentials. In this study, we present a refinement to the set of torsional parameters in the General Amber Force Field (gaff) used to calculate the potential energy of mono, di-, and gem-fluorinated nucleosides. The parameters were optimized to reproduce the pseudorotation phase angle and relative energies of a diverse set of mono- and difluoro substituted furanose ring systems using quantum mechanics umbrella sampling techniques available in the IpolQ engine in the Amber suite of programs. The parameters were developed to be internally consistent with the gaff force field and the TIP3P water model. The new set of angle and dihedral parameters and partial charges were validated by comparing the calculated phase angle probability to those obtained from experimental nuclear magnetic resonance experiments.
Emodin Combined with Multiple Low-frequency Low-intensity Ultrasound to Relieve Osteomyelitis Through Sonoantimicrobial Chemotherapy
Authors: Lu Feng , Wu Xinhui , Hu Huiqun , He Zixuan , Sun Jiacheng , Zhang Jiapeng , Song Xiaoting , Jin Xiangang , Chen Guofu
Published: January 2022

Treatment of osteomyelitis is still challenging as conventional antibiotic therapy is limited by the emergence of resistant strains and the formation of biofilms. Sonoantimicrobial chemotherapy (SACT) is a novel therapy of low-frequency and low-intensity ultrasound (LFLIU) combined with sonosensitizer. Therefore, in our study, a sonosensitizer named emodin (EM) was proposed to be combined with LFLIU to relieve acute osteomyelitis caused by Methicillin-resistant Staphylococcus aureus (MRSA) through synergistic antibacterial and anti-biofilm effects. The efficiency of different intensities of ultrasound, single (S-LFLIU, 15 min) and multiple ultrasound (M-LFLIU, 5 min every 4 h, three times) against bacteria and biofilm was compared, contributing to develop the best treatment regimen. Our results demonstrated that EM plus S-LFLIU or M-LFLIU (EM+S-LFLIU or EM+M-LFLIU) have significant synergetic bactericidal and anti-biofilm effects and EM+M-LFLIU exhibits superior performance in anti-biofilm. Furthermore, it was suggested that EM+M-LFLIU could produce a large amount of reactive oxygen species (ROS), destroy the integrity of bacterial membrane and wall, down-regulate the expression of oxidative stress, membrane wall synthesis, bacterial virulence and other related genes (agrB, PBP3, sgtB, GMK, zwf, msrA). In vivo study, micro-CT, H&E staining, ELISA assay and bacterial quantification of bone tissue indicated that EM+M-LFLIU could also relieve osteomyelitis of MRSA infection. Our work proffers an original treating bacterial osteomyelitis approach that weakens drug-resistant bacterial and suppresses biofilm formation through SACT, which may provide new prospects for clinical treatment.
Effect of SARS-CoV-2 spike mutations on its activation by TMPRSS2 and TMPRSS13
Authors: Stevaert Annelies , Van Berwaer Ria , Raeymaekers Valerie , Laporte Manon , Naesens Lieve
Published: January 2022

The continuous emergence of new SARS-CoV-2 variants urges better understanding of the functional motifs in the spike (S) protein and their tolerance towards mutations. We here focus on the S2’ motif which, during virus entry, requires cleavage by a cell surface protease to release the fusion peptide. Though belonging to an immunogenic region, the SARS-CoV-2 S2’ motif (811-KPSKR-815) has shown hardly any variation, with its three basic (K/R) residues being >99.99% conserved thus far. By creating a series of mutant S-pseudotyped viruses, we show that K814, which precedes the scissile R815 residue, is dispensable for SARS-CoV-2 spike activation by TMPRSS2 but not TMPRSS13. The latter protease lost its activity towards SARS-CoV-2 S when the S2’ motif was swapped with that of the low pathogenic 229E coronavirus (685-RVAGR-689) and also the reverse effect was seen. This swap had no impact on TMPRSS2 activation. Also in the MERS-CoV spike, introducing a dibasic scissile motif was fully accepted by TMPRSS13 but less so by TMPRSS2. Our findings are the first to demonstrate which S2’ residues are important for SARS-CoV-2 spike activation by these two airway proteases, with TMPRSS13 exhibiting higher preference for K/R rich motifs than TMPRSS2. This preemptive insight can help to estimate the impact of S2’ motif changes as they may appear in new SARS-CoV-2 variants.

IMPORTANCE

Since the start of the COVID-19 pandemic, SARS-CoV-2 is undergoing worldwide selection with frequent appearance of new variants. The surveillance would benefit from proactive characterization of the functional motifs in the spike protein, the most variable viral factor. This is linked to immune evasion but also influences spike functioning in a direct manner. Remarkably, though located in a strong immunogenic region, the S2’ cleavage motif has, thus far, remained highly conserved. This suggests that its amino acid sequence is critical for spike activation by airway proteases. To investigate this, we assessed which S2’ site mutations affect processing by TMPRSS2 and TMPRSS13, two main activators of the SARS-CoV-2 spike. Being the first in its kind, our study will help to assess the biological impact of S2’ site variations as soon as they are detected during variant surveillance.
Risk factors and survival in patients with COVID-19 in northeastern Brazil
Authors: Fernandes Ana Tereza do N S F , Rodrigues Eujessika K. , Araújo Eder R. , Formiga Magno F. , Sá Horan Priscilla K. , Ferreira Ana Beatriz N. S. , Barbosa Humberto A. , Barbosa Paulo S.
Published: January 2022

BACKGROUND

Countries have focused research on developing strategies to fight COVID-19, prevent hospitalizations, and maintain economic activities.

OBJECTIVE

This study aimed to establish a survival analysis and identify risk factors for patients with COVID-19 in a upper middle-income city in Brazil.

METHODS

We performed a retrospective cohort study with 280 hospitalized patients with COVID-19. The eCOVID platform provided data used to monitor COVID-19 cases and help communication between professionals.

RESULTS

Survival analysis showed that age ≥ 65 years was associated with decreased survival (54.8%). Females had lower survival rate than males (p=0.01). Regarding risk factors, urea concentration (p<0.001), hospital LOS (p=0.002), oxygen concentration (p=0.005), and age (p=0.02) were associated with death.

CONCLUSION

Age, hospital LOS, high blood urea concentration, and low oxygen concentration were associated with death by COVID-19 in the studied population. These findings corroborate with studies conducted in research centers worldwide.

Key Findings

Some parameters assessed during hospital admission may identify patients with COVID-19 with high risk of progressing to severe conditions and early identification of risk factors and continuous monitoring of laboratory tests may prevent progression to severe disease.

Key Implications

Knowledge regarding main signs and symptoms of COVID-19 and associated risk factors helps the population manage and monitor the disease at home and identify early signs of severity. Also, more information about COVID-19, such as prevalence, specific characteristics in certain regions, and treatments, must become public to encourage the population to participate in the control and contingency of the pandemic.
COVID-19 vaccine attitude and its predictors among people living with chronic health conditions in Ibadan, Nigeria
Authors: Ojewale Lucia Yetunde , Afolabi Rotimi Felix , Ogunniyi Adesola
Published: January 2022

Abstracts

Background

Globally COVID-19 has caused death among millions of people and new cases continue to be reported daily, including in Nigeria. With the efforts of the Nigerian government to ensure everyone gets vaccinated, the vaccination attitude and its predictors among persons with chronic health conditions remains unclear. The study was therefore conducted to assess vaccination attitude and determine its associated factors among people living with chronic health conditions.

Methods

A descriptive cross-sectional study was conducted among 423 patients attending the medical outpatient clinic of University College Hospital, Ibadan, Oyo State, Nigeria; before COVID-19 vaccination commencement. Data were collected on socio-demographic and COVID-19 related characteristics, via Open Data Kit (ODK) software. The Vaccine Attitude Examination (Vax) Scale including its four subscales was adopted to assess attitude towards COVID-19 vaccine uptake. The main outcome was vaccine attitude status defined as positive if a VAX sum score was above the median value; otherwise, non-positive’. Data were analysed using Chi-square and multivariate logistic regression analyses at 5% significance level.

Results

Hypertension (27.4%), diabetes mellitus (22.0%) and heart conditions/diseases (19.6%) were the top three conditions being managed by the participants. The overall proportion of patients with a positive attitude towards the uptake of COVID-19 vaccination was 46.6%; while 29.6% trusted the vaccine benefit, 46.6% were not worried about the aftermath effect of the vaccine and 11.1% were not concerned about the vaccine commercial profiteering. Factors associated with overall vaccine attitude were level of education, income, knowledge of COVID-19, living room arrangement, and confidence in government (p<0.05). The main influential factor on general vaccine positive attitude and the four subscales was confidence in the government.

Conclusion

Less than half of people living with a chronic medical condition had a positive attitude towards the COVID vaccine. The attitudes are mediated strongly by confidence in the government and several sociodemographic and COVID related characteristics. A lot still needs to be done to achieve the prescribed herd immunity.
A machine learning approach to identifying important features for achieving step thresholds in individuals with chronic stroke
Authors: Miller Allison E. , Russell Emily , Reisman Darcy S. , Kim Hyosub E. , Dinh Vu
Published: January 2022

Background

While many factors are associated with stepping activity after stroke, there is significant variability across studies. One potential reason for this variability is that there are some characteristics necessary to achieve greater stepping activity that differ from others that may need to be targeted to improve stepping activity.

Objective

Using two step thresholds (2500 steps/day, corresponding to home vs. community ambulation and 5500 steps/day, corresponding to achieving physical activity guidelines through walking), we applied 3 different algorithms to determine which predictors are most important to achieve these thresholds.

Methods

We analyzed data from 268 participants with stroke that included 25 demographic, performance-based and self-report variables. Step 1 of our analysis involved dimensionality reduction using lasso regularization. Step 2 applied drop column feature importance to compute the mean importance of each variable. We then assessed which predictors were important to all 3 mathematically unique algorithms.

Results

The number of relevant predictors was reduced from 25 to 7 for home vs. community and from 25 to 16 for aerobic thresholds. Drop column feature importance revealed that 6 Minute Walk Test and speed modulation were the only variables found to be important to all 3 algorithms (primary characteristics) for each respective threshold. Other variables related to readiness to change activity behavior and physical health, among others, were found to be important to one or two algorithms (ancillary characteristics).

Conclusions

Addressing physical capacity is necessary but not sufficient to achieve important step thresholds, as ancillary characteristics, such as readiness to change activity behavior and physical health may also need to be targeted. This delineation may explain heterogeneity across studies examining predictors of stepping activity in stroke.
Application of biophysical methods for improved protein production and characterization: a case study on an HtrA-family bacterial protease
Authors: Ronzetti Michael , Baljinnyam Bolormaa , Jalal Ishrat , Pal Utpal , Simeonov Anton
Published: January 2022

The high temperature requirement A (HtrA) serine protease family presents an attractive target class for antibacterial therapeutics development. These proteins possess dual protease and chaperone functions and contain numerous binding sites and regulatory loops, displaying diverse oligomerization patterns dependent on substrate type and occupancy. HtrA proteins that are natively purified coelute with contaminating peptides and activating species, shifting oligomerization and protein structure to differently activated populations. Here, a redesigned HtrA production results in cleaner preparations with high yields by overexpressing and purifying target protein from inclusion bodies under denaturing conditions, followed by a high-throughput screen for optimal refolding buffer composition using function-agnostic biophysical techniques that do not rely on target-specific measurements. We use the Borrelia burgdorferi HtrA to demonstrate the effectiveness of our function-agnostic approach, while characterization with both new and established biophysical methods shows the retention of proteolytic and chaperone activity of the refolded protein. This systematic workflow and toolset will translate to the production of HtrA-family proteins in higher quantities of pure and monodisperse composition than the current literature standard, with applicability to a broad array of protein purification strategies.

Statement

The production of a therapeutically-relevant protein family sensitive to coeluting contaminants is greatly improved by optimized expression and refolding workflow. A miniaturized, high-throughput system supported by a function-agnostic biophysics assay and modified data analysis scripts results in a refolded protein that is highly pure, monodisperse, and retains proteolytic and chaperone activity. This approach has broad applicability towards hard-to-express proteins and proteins sensitive to coeluting species. Additionally, novel methods are presented to characterize protein chaperone activity.
TheVibrio vulnificusstressosome is dispensable in nutrient-replete conditions
Authors: Cutugno Laura , Mc Cafferty Jennifer , Pané-Farré Jan , O’Byrne Conor , Boyd Aoife
Published: January 2022

The stressosome is a protein complex that has been demonstrated to sense environmental stresses and mediate the stress response in several Gram-positive bacteria, through the activation of the alternative sigma factor SigB. The in vivocharacterisation of this complex has never been performed inVibrio vulnificusor any other bacteria that do not possess SigB. The elucidation of the role of the stressosome inV. vulnificuswould provide elements to elaborate a functional model of the complex in a Gram-negative bacterium and identify the regulatory output in the absence of SigB. The stressosome locus is only found in 44% ofVibrio vulnificusisolates raising the question as to whether the role of stressosome is essential or modulatory in this bacterial species.

In this work, the expression of the stressosome genes was proven in nutrient-replete conditions and the co-transcription as one operonic unit of the stressosome locus and its putative downstream regulatory locus was demonstrated.

Moreover, the construction of a stressosome mutant lacking the four genes constituting the stressosome complex allowed us to examine the role of this complexin vivo. The initial established mutagenesis strategy relied on rifampicin-resistantV. vulnificusto select recombinant bacteria. Our data clearly showed that the influence of the RifRallele on stress and virulence characteristics overshadowed any effects of the stressosome. Therefore, we established an alternative mutagenesis strategy with a non-modifiedV. vulnificusparental strain and a DAP auxotrophicE. colidonor strain. Extensive phenotypic characterisation of the successfully-generated mutant in nutrient-replete conditions showed that the stressosome does not significantly contribute to the growth, ofV. vulnificus. The stressosome did not modulate the response ofV. vulnificusto the range of stresses tested – Ethanol, osmolarity, temperature, and salinity. Furthermore, the stressosome is dispensable for motility and exoenzyme production ofV. vulnificus.
In silico analysis of the human milk oligosaccharide glycome reveals key enzymes of their biosynthesis
Authors: McDonald Andrew G. , Mariethoz Julien , Davey Gavin P. , Lisacek Frédérique
Published: January 2022

Human milk oligosaccharides (HMOs) form the third most abundant component of human milk and are known to convey several benefits to the neonate, including protection from viral and bacterial pathogens, training of the immune system, and influencing the gut microbiome. As HMO production during lactation is driven by enzymes that are common to other glycosylation processes, we adapted a model of mucin-type GalNAc-linked glycosylation enzymes to act on free lactose. We identified a subset of 11 enzyme activities that can account for 206 of 226 distinct HMOs isolated from human milk, and constructed a biosynthetic reaction network that identifies 5 new core HMO structures. A comparison of monosaccharide compositions demonstrated that the model was able to discriminate between two possible groups of intermediates between major subnetworks, and to assign possible structures to several previously uncharacterised HMOs. The effect of enzyme knockouts is presented, identifying β-1,4-galactosyltransferase and β-1,3-N-acetylglucosaminyltransferase as key enzyme activities involved in the generation of the observed HMO glycosylation patterns. The model also provides a synthesis chassis for the most common HMOs found in lactating mothers.
A wheat kinase and immune receptor form the host-specificity barrier against the blast fungus
Authors: Arora Sanu , Steed Andrew , Goddard Rachel , Gaurav Kumar , O’Hara Tom , Schoen Adam , Rawat Nidhi , Elkot Ahmed F. , Chinoy Catherine , Nicholson Martha H. , Asuke Soichiro , Steuernagel Burkhard , Yu Guotai , Awal Rajani , Forner-Martínez Macarena , Wingen Luzie , Baggs Erin , Clarke Jonathan , Krasileva Ksenia V. , Tosa Yukio , Jones Jonathan D. G. , Tiwari Vijay K. , Wulff Brande B. H. , Nicholson Paul
Published: January 2022

Since emerging in Brazil in 1985, wheat blast has spread throughout South America and recently appeared in Bangladesh and Zambia. We show that two wheat resistance genes, Rwt3 and Rwt4, acting as host-specificity barriers against non-Triticum blast pathotypes encode a nucleotide-binding leucine-rich repeat immune receptor and a tandem kinase, respectively. Molecular isolation of these genes allowed us to develop assays that will ensure the inclusion of these two genes in the wheat cultivars to forestall the recurrence of blast host jumps.
Pyrrole produced byPseudomonas aeruginosainfluences olfactory food choice ofCaenorhabditis elegans
Authors: Prakash Deep , Siddiqui Ritika , Chalasani Sreekanth H. , Singh Varsha
Published: January 2022

Sense of smell can influence dietary choices in animals. So far, most of the research has focused on how animals respond to distinct odors when they are introduced individually. However, it remains unclear how animals evaluate foods that contain a bouquet of olfactory cues with contrasting effects. Here, we utilizeCaenorhabditis elegansas a bacterivore to ask if odors produced by dietary bacteria can regulate worms’ food preferences. We show that the bacteriumPseudomonas aeruginosaproduces a relatively small quantity of a new attractant forC. elegans. We identify the odor as a heterocyclic compound called pyrrole. We find that pyrrole contributes to the sensory decision-making of worms in diet preference assays. Using specific neuronal ablation lines and calcium response assays, we show that AWA odor sensory neurons of worms are necessary for sensing pyrrole. In all, we show that specific odors produced by bacteria can influence food choice behavior of animals.
Biocompatible fluorocarbon liquid underlays for in situ extraction of isoprenoids from microbial cultures
Authors: Overmans Sebastian , Lauersen Kyle J.
Published: January 2022

Microbial production of heterologous metabolites is now a mature technology in many host organisms, opening new avenues for green production processes for specialty chemicals. At lab scale, petroleum-based hydrophobic bio-compatible solvents like dodecane can be used as a second phase on top of microbial cultures to act as a physical sink for heterologous hydrocarbon products like isoprenoids. However, this approach has significant drawbacks at scale due to the difficulty of handling solvents and their potential contamination with unwanted byproducts of their manufacture. We discovered that synthetic perfluorocarbon liquids (FCs), commonly used for heat transfer, can also act as physical sinks for microbially produced isoprenoid compounds. FCs are stable, inert, and are amenable to direct liquid-liquid extraction with alcohols for rapid product isolation. These liquids are more dense than water and form a lower phase to microbial cultures rather than an upper phase as with other solvents. Their ability to form an under-layer or ‘underlay’ also enables the cultivation of microbes directly at the FC-culture medium interface via gravity settling, which could open their application for filamentous or mat-forming organisms. We present comparisons of the isoprenoid extraction potential of three commercial FCs: FC-3283, FC-40, and FC-770 with engineered green microalga cultures producing patchoulol, taxadiene, casbene, or 13R(+) manoyl oxide. We demonstrate that FCs are promising alternatives to traditional solvents and open new avenues in bio-process design for microbial heterologous metabolite milking.
The antimicrobial peptide cathelicidin is critical for the development of Th17 responses in severe inflammatory disease
Authors: Smith Katie J , Minns Danielle , McHugh Brian J , Holloway Rebecca K. , O’Connor Richard , Williams Anna , Melrose Lauren , McPherson Rhoanne , Miron Veronique E. , Davidson Donald J , Findlay Emily Gwyer
Published: January 2022

Multiple Sclerosis (MS) is a highly prevalent demyelinating autoimmune condition; the mechanisms regulating its severity and progression are unclear. The IL-17-producing Th17 subset of T cells has been widely implicated in MS and in the mouse model, experimental autoimmune encephalomyelitis (EAE). However, the differentiation and regulation of Th17 cells during EAE remain incompletely understood. Although evidence is mounting that the antimicrobial peptide cathelicidin profoundly affects early T cell differentiation, no studies have looked at its role in longer term T cell responses. Now, we report that cathelicidin drives severe EAE disease. It is released from neutrophils, microglia and endothelial cells throughout disease; its interaction with T cells potentiates Th17 differentiation in lymph nodes and Th17 to exTh17 plasticity and IFN-γ production in the spinal cord. As a consequence, mice lacking cathelicidin are protected from severe EAE. In addition, we show that cathelicidin is produced by the same cell types in the active brain lesions in human MS disease. We propose that cathelicidin exposure results in highly activated, cytokine-producing T cells which drive autoimmunity; this is a mechanism through which neutrophils amplify inflammation in the central nervous system.
Tracking human skill learning with a hierarchical Bayesian sequence model
Authors: Éltető Noémi , Nemeth Dezső , Janacsek Karolina , Dayan Peter
Published: January 2022

Humans can implicitly learn complex perceptuo-motor skills over the course of large numbers of trials. This likely depends on our becoming better able to take advantage of ever richer and temporally deeper predictive relationships in the environment. Here, we offer a novel characterization of this process, fitting a non-parametric, hierarchical Bayesian sequence model to the reaction times of human participants’ responses over ten sessions, each comprising thousands of trials, in a serial reaction time task involving higher-order dependencies. The model, adapted from the domain of language, forgetfully updates trial-by-trial, and seamlessly combines predictive information from shorter and longer windows onto past events, weighing the windows proportionally to their predictive power. As the model defines a prior over window depths, we were able to determine the extent to which the internal predictions of individual participant depended on how many previous elements.

Already in the first session, the model showed that participants had begun to rely on two previous elements (i.e., trigrams), thereby successfully adapting to the most prominent higher-order structure in the task. The extent to which local statistical fluctuations influenced participants’ responses waned over subsequent sessions, as subjects forgot the trigrams less and evidenced skilled performance. By the eighth session, a subset of participants shifted their prior further to consider a context deeper than two previous elements. Finally, participants showed resistance to interference and slow forgetting of the old sequence when it was changed in the final sessions. Model parameters for individual subjects covaried appropriately with independent measures of working memory. In sum, the model offers the first principled account of the adaptive complexity and nuanced dynamics of humans’ internal sequence representations during long-term implicit skill learning.

Author summary

A central function of the brain is to predict. One challenge of prediction is that both external events and our own actions can depend on a variably deep temporal context of previous events or actions. For instance, in a short motor routine, like opening a door, our actions only depend on a few previous ones (e.g., push the handle if the key was turned). In longer routines such as coffee making, our actions require a deeper context (e.g., place the moka pot on the hob if coffee is ground, the pot is filled and closed, and the hob is on). We adopted a model from the natural language processing literature that matches humans’ ability to learn variable-length relationships in sequences. This model explained the gradual emergence of more complex sequence knowledge and individual differences in an experiment where humans practiced a perceptual-motor sequence over 10 weekly sessions.
Molecular mechanisms of Plasmodium development in male and female Anopheles mosquitoes
Authors: Haraguchi Asako , Takano Makoto , Hakozaki Jun , Nakayama Kazuhiko , Nakamura Sacré , Yoshikawa Yasunaga , Fukumoto Shinya , Kusakisako Kodai , Ikadai Hiromi
Published: January 2022

Vector competence influences the ability of Anopheles mosquitoes to transmit Plasmodium parasites. The aim of this study was to determine the competence of male and female Anopheles mosquitoes to support the development of Plasmodium parasites. Male and female A. stephensi (STE2 strain) were infected with in vitro-cultured P. berghei (ANKA strain) ookinetes. We found that the number of oocysts produced was higher in males than in females. RNA-seq analysis of male and female mosquitoes injected with P. berghei ookinetes showed that predominantly genes of unknown function changed in expression levels in response to ookinete infection; however, further studies are required to elucidate their functions. Moreover, male mosquitoes were injected with in vitro-cultured P. falciparum (3D7 strain) gametocytes or zygotes. The development of P. falciparum in males was detected using nested polymerase chain reaction. We found the DNA content was higher on day 15 than on day 0, indicating that P. falciparum developed in the mosquito hemocoel. This study revealed promising new mechanisms underlying the interactions between Plasmodium and mosquitoes.

Author Summary

Anopheles mosquitoes transmit Plasmodium parasites that cause malaria disease. Vector competence is the ability of vectors to support pathogen development. The aim of this study was to determine the competence of male and female mosquitoes for Plasmodium parasites. Oocysts were formed in both male and female mosquitoes injected with ookinetes from in vitro-cultured Plasmodium berghei, which causes malaria in mice. The number of oocysts was higher in males, indicating that the competence in males was higher than that in females. RNA-seq analysis showed that the expression of genes of unknown function was highly variable in males and females. The genes defining the competence factors need further study, but the results indicate novel genes may be discovered. Furthermore, the development of Plasmodium falciparum, which causes the most severe malaria in humans, in male mosquitoes injected with in vitro-cultured gametocytes or zygotes was detected. As male mosquitoes do not suck blood, this method may allow us to experiment with Plasmodium more safely.
Three-dimensional actuation of hummingbird wings requires diverse effects from the primary flight muscles
Authors: Agrawal Suyash , Tobalske Bret W. , Anwar Zafar , Luo Haoxiang , Hedrick Tyson L. , Cheng Bo
Published: January 2022

Hummingbirds have evolved to hover and maneuver with exceptional flight control. This is directly enabled by their musculoskeletal system that successfully exploits the agile motion of flapping wings. Here, we reveal novel principles of hummingbird wing actuation that provide insights into the evolution and robotic emulation of hummingbird flight. We develop a functional model of hummingbird musculoskeletal system, which predicts instantaneous, three-dimensional torque produced by primary (pectoralis and supracoracoideus) and combined secondary muscles. It also reveals primary muscle contractile behavior, including stress, strain, elasticity, and work. Results show that the primary muscles (i.e., the flight “engine”) function as diverse effectors, as they do not simply power the stroke, but also actively deviate and pitch the wing. The secondary muscles produce controlled-tightening effects, by acting against primary muscles in deviation and pitching. The diverse effector capacity of pectoralis is associated with the evolution of a comparatively enormous bicipital crest on humerus.
Geographical and ecological drivers of coexistence dynamics in squamate reptiles
Authors: Alencar Laura R. V. , Quental Tiago B.
Published: January 2022

Abstract

Aim

Species richness varies widely across space. To understand the processes behind these striking patterns, we must know what are the relevant drivers underlying species coexistence. Several factors can potentially shape species coexistence such as the speciation process, the time since divergence between lineages, environmental effects, and intrinsic properties of the organisms. For the first time, we model the coexistence dynamics of lizards and snakes across broad temporal and spatial scales, investigating the role of species interactions, dispersal ability, and geographic area.

Location

Global

Time period

Last 20 million years

Major taxa studied

Squamata (lizards and snakes)

Methods

We used 448 closely related species pairs and their age since divergence across 100 dated phylogenies. We categorized each pair as sympatric or allopatric and as occurring on islands or continents. We measured morphological traits to quantify niche divergence and used range and body size as proxies for dispersal ability. We applied a model-comparison framework in lizards and snakes separately to evaluate which factors best explained their coexistence dynamics.

Results

We found that distinct factors drive the coexistence dynamics in lizards and snakes. In snakes, species pairs that coexist tend to occur on islands and are more different in body size, suggesting that both geographical setting and species interactions might be relevant factors. In contrast, we only found evidence that dispersal ability shaped the coexistence of lizards, where species coexist when they have higher dispersal abilities.

Main conclusions

Lizards and snakes greatly differ in coexistence dynamics. Higher heterogeneity in coexistence dynamics within lizards and group-specific life-history aspects might help to explain these findings. Our results emphasize that the interaction between where organisms are and who they are, ultimately shapes biodiversity patterns. We also highlight interesting avenues for further studies on species coexistence in deep time.
DiSCs – Domains involving SETDB1 and Cohesin are critical regulators of genome topology and stem cell fate
Authors: Warrier Tushar , El Farran Chadi , Zeng Yingying , Ho Benedict Shao Quan , Xu Don Loi , Bao Qiuye , Zheng Zi Hao , Bi Xuezhi , Tan Kelly Yu Sing , Ng Huck Hui , Ong Derrick Sek Tong , Chu Justin Jang Hann , Sanyal Amartya , Fullwood Melissa Jane , Collins James , Li Hu , Xu Jian , Loh Yuin-Han
Published: January 2022

SETDB1 is a key regulator of lineage-specific genes and endogenous retroviral elements (ERVs) through its deposition of repressive H3K9me3 mark. Apart from its H3K9me3 regulatory role, SETDB1 has seldom been studied in terms of its other potential regulatory roles. To investigate this, a genomic survey of SETDB1 binding in mouse embryonic stem cells across multiple libraries was conducted, leading to the unexpected discovery of regions bereft of common repressive histone marks (H3K9me3, H3K27me3). These regions were enriched with the CTCF motif that is often associated with the topological regulator Cohesin. Further profiling of these non-H3K9me3 regions led to the discovery of a cluster of non-repeat loci that were co-bound by SETDB1 and Cohesin. These regions, which we named DiSCs (Domains involving SETDB1 and Cohesin) were seen to be proximal to the gene promoters involved in embryonic stem cell pluripotency and lineage development. Importantly, it was found that SETDB1-Cohesin co-regulate target gene expression and genome topology at these DiSCs. Depletion of SETDB1 led to localized dysregulation of Cohesin binding thereby locally disrupting topological structures. Dysregulated gene expression trends revealed the importance of this cluster in ES cell maintenance as well as at gene ‘islands’ that drive differentiation to other lineages. The ‘unearthing’ of the DiSCs thus unravels a unique topological and transcriptional axis of control regulated chiefly by SETDB1.
Common and lifestyle-specific traits of mycorrhiza-associated metabolite alterations in plant roots reflects strategies of root-mycorrhizal interactions
Authors: Xia Mengxue , Suseela Vidya , McCormack M. Luke , Kennedy Peter G. , Tharayil Nishanth
Published: January 2022

Convergent patterns in morphological and genetic traits of mycorrhizas have been well-documented and reflect common selection forces that define mycorrhizas. However, generalizable patterns of mycorrhiza-associated chemical alterations, which are immediately linked to plant and fungal strategies for successful symbiosis, have yet to be emerged. Comparing root metabolomes of phylogenetically-diverse plants inoculated by mycorrhizal fungi across two major lifestyles (arbuscular- vs. ecto-mycorrhizas), our study uncovers metabolite changes unique to each mycorrhizal lifestyle and those common across plant-mycorrhizal combinations irrespective of lifestyles. Arbuscular and ecto- mycorrhizal colonized roots accumulated different sets of carbohydrates, indicating unique carbon partitioning strategies: particularly, arbuscular mycorrhizal roots accumulated cyclic polyols inaccessible for symbionts, suggesting tighter regulation of plants in carbon partitioning. Mycorrhizas also altered specialized metabolism, featuring frequent increases of flavan-3-ols and decreases of flavanols irrespective of mycorrhizal lifestyles, suggesting tactical reconfiguration of specialized metabolites to facilitate/contain symbiosis. Our data show for the first time, to our knowledge, that part of the root metabolite alterations by mycorrhizas were relatively common across plant-mycorrhizal systems, highlighting their potentially critical regulatory and evolutionary role for successful symbiosis. This commonality appears robust to phylogenetic diversity of host plants and thus may be widespread in land plants. Our findings offer future research venues to elucidate the finer roles of these common traits of mycorrhiza-associated metabolite alterations and thus help to eventually develop a comprehensive understanding of this omnipresent plant-fungus partnership.
Sensing Echoes: Temporal Misalignment in Auditory Brainstem Responses as the Earliest Marker of Neurodevelopmental Derailment
Authors: Torres Elizabeth B , Varkey Hannah , Vero Joe , London Eric , Phan Ha , Kittler Phyllis , Gordon Anne , Delgado Rafael E. , Delgado Christine F. , Simpson Elizabeth A.
Published: January 2022

Neurodevelopmental disorders are on the rise worldwide, with diagnoses that detect derailment from typical milestones by 3-4.5 years of age. By then, the circuitry in the brain has already reached some level of maturation that inevitably takes neurodevelopment through a different course. There is a critical need then to develop analytical methods that detect problems much earlier and identify targets for treatment. We integrate data from multiple sources, including neonatal auditory brainstem responses (ABR), clinical criteria detecting autism years later in those neonates, and similar ABR information for young infants and children who also received a diagnosis of autism spectrum disorders, to produce the earliest known digital screening biomarker to flag neurodevelopmental derailment in neonates. This work also defines concrete targets for treatment and offers a new statistical approach to aid in guiding a personalized course of maturation in line with the highly nonlinear, accelerated neurodevelopmental rates of change in early infancy.

Significance Statement

Autism is currently detected on average after 4.5 years of age, based on differences in social interactions. Yet basic building blocks that develop to scaffold social interactions are present at birth and quantifiable at clinics. Auditory Brainstem Response tests, routinely given to neonates, infants, and young children, contain information about delays in signal transmission important for sensory integration. Although currently discarded as gross data under traditional statistical approaches, new analytics reveal unambiguous differences in ABR signals’ fluctuations between typically developing neonates and those who received an autism diagnosis. With very little effort and cost, these new analytics could be added to the clinical routine testing of neonates to create a universal screening tool for neurodevelopmental derailment and prodrome of autism.
Ultraviolet Dosage and Decontamination Efficacy was Widely Variable across 14 UV Devices after Testing a Dried Enveloped Ribonucleic Acid Virus Surrogate for SARS-CoV-2
Authors: Buhr Tony L. , Borgers-Klonkowski Erica , Gutting Bradford W. , Hammer Emlyn E. , Hamilton Shelia M. , Huhman Brett M. , Jackson Stuart L. , Kennihan Neil L. , Lilly Samuel D. , Little John D. , Luck Brooke B. , Matuczinski Emily A. , Miller Charles T. , Sides Rachel E. , Yates Vanessa L. , Young Alice A.
Published: January 2022

Abstract

Aims

The dosages and efficacy of 14 ultraviolet (UV) decontamination technologies were measured against a SARS-CoV-2 surrogate virus that was dried on to different materials for lab and field testing.

Methods and Results

A live enveloped, ribonucleic acid (RNA) virus surrogate for SARS- CoV-2 was dried on stainless steel 304 (SS304), Navy Top Coat-painted SS304 (NTC), cardboard, polyurethane, polymethyl methacrylate (PMMA), and acrylonitrile butadiene styrene (ABS) at > 8.0 log10 plaque-forming units (PFU) per test coupon. The coupons were then exposed to UV radiation during both lab and field testing. Commercial and prototype UV- emitting devices were measured for efficacy: 4 handheld devices, 3 room/surface-disinfecting machines, 5 air-disinfection devices, and 2 larger custom-made machines. UV device dosages ranged from 0.01-729 mJ cm-2. Anti-viral efficacy among the different UV devices ranged from no decontamination up to nearly achieving sterilization. Importantly, cardboard required far more dosage than SS304.

Conclusions

Enormous variability in dosage and efficacy was measured among the different UV devices. Porous materials limit the utility of UV decontamination.

Significance and Impact of the Study

UV devices have wide variability in dosages, efficacy, hazards, and UV output over time indicating that each UV device needs independent technical measurement and assessment for product development, prior to, and during use.
Rewiring of aminoacyl-tRNA synthetase localization and interactions in plants with extensive mitochondrial tRNA gene loss
Authors: Warren Jessica M. , Broz Amanda K. , Martinez-Hottovy Ana , Elowsky Christian , Christensen Alan C. , Sloan Daniel B.
Published: January 2022

The number of tRNAs encoded in plant mitochondrial genomes varies considerably. Ongoing loss of bacterial-like mitochondrial tRNA genes in many lineages necessitates the import of nuclear-encoded eukaryotic counterparts that share little sequence similarity. Because tRNAs are involved in highly specific molecular interactions, this replacement process raises questions about the identity and trafficking of enzymes necessary for the maturation and function of newly imported tRNAs. In particular, the aminoacyl-tRNA synthetases (aaRSs) that charge tRNAs are usually divided into distinct classes that specialize on either organellar (mitochondrial and plastid) or cytosolic tRNAs. Here, we investigate the evolution of aaRS subcellular localization in a plant lineage (Sileneae) that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts (PacBio Iso-Seq), we found the predicted retargeting of many ancestrally cytosolic aaRSs to the mitochondrion and confirmed these results with colocalization microscopy assays. However, we also found cases where aaRS localization does not appear to change despite functional tRNA replacement, suggesting evolution of novel interactions and charging relationships. Therefore, the history of repeated tRNA replacement inSileneaemitochondria reveals that differing constraints on tRNA/aaRS interactions may determine which of these alternative coevolutionary paths is used to maintain organellar translation in plant cells.
Shade-induced transcription of PIF-Direct-Target Genes precedes H3K4-trimethylation chromatin modification rises
Authors: Calderon Robert H. , Dalton Jutta , Zhang Yu , Quail Peter H.
Published: January 2022

The phytochrome (phy)-PIF (Phytochrome Interacting Factor) sensory module perceives and transduces light signals to Direct-Target Genes (DTGs), which then drive the adaptational responses in plant growth and development, appropriate to the prevailing environment. These signals include the first exposure of etiolated seedlings to sunlight upon emergence from subterranean darkness, and the change in color of the light that is filtered through, or reflected from, neighboring vegetation (‘shade’). Previously, we identified three broad categories of rapidly signal-responsive genes: those repressed by light and conversely induced by shade; those repressed by light, but subsequently unresponsive to shade; and those responsive to shade only. Here, we investigate the potential role of epigenetic chromatin modifications in regulating these contrasting patterns of phy-PIF module-induced expression of DTGs. Using RNA-seq and ChlP-seq, time-resolved profiling of transcript and histone 3 lysine 4 trimethylation (H3K4me3) levels, respectively, we show that, whereas the initial dark-to-light transition triggers a rapid, apparently temporally-coincident decline of both parameters, the light-to-shade transition induces similarly rapid increases in transcript levels that precede increases in H3K4me3 levels. Together with other recent findings, these data raise the possibility that, rather than being causal in the shade-induced expression changes, H3K4me3 may function to buffer the rapidly fluctuating shade/light switching that is intrinsic to vegetational canopies under natural sunlight conditions.