bluuebunny/crossref_metadata_2025 huggingface dataset:
Walk the Plank! Using mobile EEG to investigate emotional lateralization of immersive fear in virtual reality
Authors: Basbasse Yasmin El , Packheiser Julian , Peterburs Jutta , Maymon Christopher , Güntürkün Onur , Grimshaw Gina , Ocklenburg Sebastian
Published: September 2022

1.

Most studies on emotion processing rely on the presentation of emotional images or films. However, this methodology lacks ecological validity, limiting the extent to which findings can generalize to emotion processing in the wild. More realistic paradigms using Virtual Reality (VR) may be better suited to investigate authentic emotional states and their neuronal correlates. This preregistered study examines the neuronal underpinnings of naturalistic fear, measured using mobile electroencephalography (EEG). Seventy-five healthy participants entered a simulation in which they walked across a virtual plank which extended from the side of a skyscraper – either 80 stories up (the negative condition) or at street level (the neutral condition). Subjective ratings showed that the negative condition induced feelings of fear and presence. Following the VR experience, subjects passively viewed negative and neutral images from the International Affective Picture system (IAPS) outside of VR. We compared frontal alpha asymmetry between the plank and IAPS task and across valence of the conditions. Asymmetry indices (AI) in the plank task revealed greater right-hemispheric lateralization during the negative VR condition, relative to the neutral VR condition and to IAPS viewing. Within the IAPS task, no significant asymmetries were detected, though AIs in the VR task and in the IAPS task were negatively correlated suggesting that stronger right-hemispheric activation in the VR task was associated with stronger left-hemispheric activation during the IAPS task. In summary, our findings indicate that immersive technologies such as VR can advance emotion research by providing more ecologically valid ways to induce emotion.
Improving fMRI in Parkinson’s Disease by Accounting for Brain Region-Specific Activity Patterns
Authors: Torrecuso Renzo , Mueller Karsten , Holiga Štefan , Sieger Tomáš , Vymazal Josef , Růžička Filip , Roth Jan , Růžička Evzen , Schroeter Matthias L. , Jech Robert , Möller Harald E.
Published: September 2022

In functional magnetic imaging (fMRI) in Parkinson’s disease (PD), a paradigm consisting of blocks of finger tapping and rest along with a corresponding general linear model (GLM) is often used to assess motor activity. However, this method has three limitations: (i) Due to the strong magnetic field and the confined environment of the cylindrical bore, it is troublesome to accurately monitor motor output and, therefore, variability in the performed movement is typically ignored. (ii) Given the loss of dopaminergic neurons and ongoing compensatory brain mechanisms, motor control is abnormal in PD. Therefore, modeling of patients’ tapping with a constant amplitude (using a boxcar function) and the expected Parkinsonian motor output are prone to mismatch. (iii) The motor loop involves structures with distinct hemodynamic responses, for which only one type of modeling (e.g., modeling the whole block of finger tapping) may not suffice to capture these structure’s temporal activation. The first two limitations call for considering results from online recordings of the real motor output that may lead to significant sensitivity improvements. This was shown in previous work using a non-magnetic glove to capture details of the patients’ finger movements in a so-called kinematic approach. For the third limitation, modeling motion initiation instead of the whole tapping block has been suggested to account for different temporal activation signatures of the motor loop’s structures. In the present study we propose improvements to the GLM as a tool to study motor disorders. For this, we test the robustness of the kinematic approach in an expanded cohort (n=31), apply more conservative statistics than in previous work, and evaluate the benefits of an event-related model function. Our findings suggest that the integration of the kinematic approach offers a general improvement in detecting activations in subcortical structures, such as the basal ganglia. Additionally, modeling motion initiation using an event-related design yielded superior performance in capturing medication-related effects in the putamen. Our results may guide adaptations in analysis strategies for functional motor studies related to PD and also in more general applications.
Durable resistance or efficient disease control? Adult Plant Resistance (APR) at the heart of the dilemma
Authors: Rimbaud Loup , Papaïx Julien , Rey Jean-François , Moury Benoît , Barrett Luke , Thrall Peter
Published: September 2022

Abstract

Adult plant resistance (APR) is an incomplete and delayed protection of plants against pathogens. At first glance, such resistance should be less efficient than classical major-effect resistance genes, which confer complete resistance from seedling stage, to reduce epidemics. However, by allowing some ‘leaky’ levels of disease, APR genes are predicted to be more durable than major genes because they exert a weaker selection pressure on pathogens towards adaptation to resistance. However, the impact of partial efficiency and delayed mode of action of APR on the evolutionary and epidemiological outcomes of resistance deployment has never been tested.

Using the demogenetic, spatially explicit, temporal, stochastic modellandsepi, this study is a first attempt to investigate how resistance efficiency, age at the time of resistance activation and target pathogenicity trait jointly impact resistance durability and disease control at the landscape scale. Our numerical experiments explore the deployment of APR in a simulated agricultural landscape, alone or together with a major resistance gene. As a case study, the mathematical model has been parameterised for rust fungi (genusPuccinia) of cereal crops, for which extensive data are available.

Our simulations confirm that weak efficiency and delayed activation of APR genes reduce the selection pressure applied on pathogens and their propensity to overcome resistance, but do not confer effective protection. On the other hand, stronger APR genes (which increase selection pressure on the pathogen) may be quickly overcome but have the potential to provide some disease protection in the short-term. This is attributed to strong competition between different pathogen genotypes and the presence of fitness costs of adaptation, especially when APR genes are deployed together with a major resistance gene via crop mixtures or rotations.
Altered population activity and local tuning heterogeneity in auditory cortex ofCacna2d3-deficient mice
Authors: Wadle Simon L. , Schmitt Tatjana T.X. , Engel Jutta , Kurt Simone , Hirtz Jan J.
Published: September 2022

The α2δ3 auxiliary subunit of voltage-activated calcium channels is required for normal synaptic transmission and precise temporal processing of sounds in the auditory brainstem. In mice its loss additionally leads to an inability to distinguish amplitude-modulated tones. Furthermore, loss of function of α2δ3 has been associated with autism spectrum disorder in humans. To investigate possible alterations of network activity in the higher-order auditory system in α2δ3 knockout mice, we analyzed neuronal activity patterns and topography of frequency tuning within networks of the auditory cortex (AC) using two-photon Ca2+imaging. Compared to wild-type mice we found distinct subfield-specific alterations in the primary auditory cortex, expressed in overall lower correlations between the network activity patterns in response to different sounds as well as lower reliability of these patterns upon repetitions of the same sound. Higher AC subfields did not display these alterations but showed a higher amount of well-tuned neurons along with lower local heterogeneity of the neurons’ frequency tuning. Our results provide new insight into AC network activity alterations in an autism spectrum disorder-associated mouse model.
Integrating sex-bias into studies of archaic admixture on chromosome X
Authors: Chevy Elizabeth T. , Huerta-Sánchez Emilia , Ramachandran Sohini
Published: September 2022

Evidence of interbreeding between archaic hominins and humans comes from methods that infer the locations of segments of archaic haplotypes, or ‘archaic coverage’ using the genomes of people living today. As more estimates of archaic coverage have emerged, it has become clear that most of this coverage is found on the autosomes— very little is retained on chromosome X. Here, we summarize published estimates of archaic coverage on autosomes and chromosome X from extant human samples. We find on average 7.9 times more archaic coverage on autosomes than chromosome X, and identify broad continental patterns in this ratio: greatest in American samples, and least in South Asian samples. We also perform extensive simulation studies to investigate how the amount of archaic coverage, lengths of coverage, and rates of purging of archaic coverage are affected by sex-bias caused by an unequal sex ratio within the archaic introgressors. Our results generally confirm that, with increasing male sex-bias, less archaic coverage is retained on chromosome X. Ours is the first study to explicitly model such sex-bias and its potential role in creating the dearth of archaic coverage on chromosome X.

Author summary

Tens of thousands of years ago, humans interbred with our close hominin relatives (e.g. Neanderthals), which we know from finding segments of archaic hominin DNA in our genomes. Up to 4% of a human genome may be archaic DNA, but most of that archaic part is on the autosomes (the non-sex chromosomes). Chromosome X usually contains 3 to 10 times less archaic DNA than the autosomes. Also unlike the autosomes, it is always passed down by mothers, but only sometimes by fathers. There are several hypotheses for why chromosome X has less archaic DNA than the autosomes; one that has not been fully explored is whether the archaic hominins that interbred with our ancestors were mostly male or mostly female, known as ‘sex-bias’. In this paper, we use simulations to investigate whether sex-bias could produce less archaic DNA on chromosome X. Using simulation studies, we find that when the archaics are mostly male, modern humans end up with less archaic DNA on chromosome X than their autosomes, compared to when there is a female-bias or no sex-bias. Therefore, male sex-bias could be contributing to the difference in the amount of archaic DNA on chromosome X versus the autosomes. Of course, there are still plenty of other factors to be explored about how demography and selection have shaped our DNA. Studying patterns like this helps us learn more about early hominin natural history, and contextualizes archaic interbreeding events among other sex-biased events in human history.
Differences in anti-viral immune responses in individuals of Indian and European origin: relevance for the COVID-19 pandemic
Authors: Geckin Büsranur , Zoodsma Martijn , Kilic Gizem , Debisarun Priya A. , Rakshit Srabanti , Adiga Vasista , Ahmed Asma , Parthiban Chaitra , Kumar Nirutha Chetan , D’Souza George , Baltissen Marijke P , Martens Joost H A , Andres Jorge Dominguez , Li Yang , Vyakarnam Annapurna , Netea Mihai G
Published: September 2022

During the COVID-19 pandemic, large differences in susceptibility and mortality due to SARS-CoV-2 infection have been reported between populations in Europe and South Asia. While both host and environmental factors (including BCG vaccination) have been proposed to explain this, the potential biological substrate of these differences is unknown. We purified peripheral blood mononuclear cells from individuals living in India and the Netherlands at baseline and 10-12 weeks after BCG vaccination. We compared chromatin accessibility between the two populations at baseline, as well as gene transcription profiles and cytokine production capacities upon viral stimulation with influenza and SARS-CoV-2. The chromatin accessibility of genes important for adaptive immunity was higher in Indians compared to Europeans, while the latter had more accessible chromatin regions in genes of the innate immune system. At the transcriptional level, we observed that Indian volunteers displayed a more tolerant immune response to viral stimulation, in contrast to a more exaggerated response in Europeans. BCG vaccination strengthened the tolerance program in Indians, but not in Europeans. These differences may partly explain the different impact of COVID-19 on the two populations.
Evolutionary states and trajectories characterized by distinct pathways stratify ovarian high-grade serous carcinoma patients
Authors: Lahtinen Alexandra , Lavikka Kari , Li Yilin , Virtanen Anni , Jamalzadeh Sanaz , Huhtinen Kaisa , Carpén Olli , Hietanen Sakari , Häkkinen Antti , Hynninen Johanna , Oikkonen Jaana , Hautaniemi Sampsa
Published: September 2022

Ovarian high-grade serous carcinoma (HGSC) is typically diagnosed at an advanced stage, with multiple genetically heterogeneous clones existing in the tumors long before therapeutic intervention. Herein we characterized HGSC evolutionary states using whole-genome sequencing data from 214 samples of 55 HGSC patients in the prospective, longitudinal, multiregion DECIDER study. Comparison of the tissues revealed that site-of-origin samples have 70% more unique clones than the metastatic tumors or ascites. By integrating clonal composition and topology of HGSC tumors we discovered three evolutionary states that represent a continuum from genomically highly variable to stable tumors with significant association to treatment response. The states and their evolutionary trajectories were characterized by unique, targetable pathways, which were validated with RNA-seq data. Our study reveals that genomic heterogeneity is unaffected by the current standard-of-care and pinpoints effective treatment targets for each group. All genomics data are available via an interactive visualization platform for rapid exploration.
Hepatic fibrosis induced zinc-deficient dermatosis in American alligators (Alligator mississippiensis)
Authors: Piras Ilaria M. , Bezuidenhout Annemarie , Díaz-Delgado Josué , Slawski Deirdre , Kelly Pamela A.
Published: September 2022

Crocodilian farming generates strong economic incentives for the conservation of several species previously endangered by intensive hunting. Ranching farms, in particular, are intimately connected to the natural crocodilian habitat and have a significant impact on wetland preservation. The financial sustainability of this industry relies on the production of first grade skins for the luxury leather market. Only flawless skins are considered of first grade by the stringent standards of the market, and even a single defect represents an economical loss. “Double scale” is one such defect that drastically reduces the appeal of crocodilian skin. Although double scale defects represent a threat to the economical sustainability of the farming industry, there is no scientific literature available on this topic. This study, carried out in a ranching farm of American alligators (Alligator mississippiensis), represents the first investigation into the pathogenesis of double scale. Our results indicate that double scale is a keratinization disorder associated with zinc deficiency. Furthermore, we found that portal hypertension due to liver fibrosis, underlies zinc deficiency in cases of double scale. Lastly, we found that chronic vitamin A toxicity can cause liver fibrosis in crocodilians. For the first time, we demonstrate a causal association between liver disease and skin quality in a crocodilian species. This study reveals the conserved role of zinc in the homeostasis of reptilian skin. Also, we show that, like mammals, reptiles may develop liver fibrosis following chronic vitamin A toxicity and through activation of hepatic stellate cells. Our results advance herpetological medicine and will translate into improved captive crocodilian welfare and husbandry.
A red fluorescent genetically encoded biosensor for extracellular L-lactate
Authors: Nasu Yusuke , Kamijo Yuki , Hashizume Rina , Sato Haruaki , Hori Yukiko , Tomita Taisuke , Drobizhev Mikhail , Campbell Robert E.
Published: September 2022

L-Lactate, traditionally recognized as a waste product of metabolism, is now appreciated as a key intercellular energy currency in mammals. To enable investigations of intercellular shuttling of L-lactate, we have previously reported eLACCO1.1, a green fluorescent genetically encoded biosensor for extracellular L-lactate. eLACCO1.1 enables cellular resolution imaging of extracellular L-lactate in cultured mammalian cells and brain tissue. However, eLACCO1.1 spectrally overlaps with commonly used optical biosensors and actuators, limiting its application for multiplexed imaging or combined use with optogenetic actuators. Here, we report a red fluorescent extracellular L-lactate biosensor, designated R-eLACCO2. R-eLACCO2 is the end-product of extensive directed evolution and exhibits a large fluorescence response to L-lactate with high molecular specificity in vitro. We demonstrate that R-eLACCO2 with optimized leader and anchor sequences shows a large fluorescence change in response to extracellular L-lactate on the membrane of live mammalian cells. R-eLACCO2 should enable multicolor imaging of extracellular L-lactate in combination with other fluorescent probes and optogenetic actuators.
Influenza virus transcription and progeny production are poorly correlated in single cells
Authors: Bacsik David J. , Dadonaite Bernadeta , Butler Andrew , Greaney Allison J. , Heaton Nicholas S. , Bloom Jesse D.
Published: September 2022

The ultimate success of a viral infection at the cellular level is determined by the number of progeny virions produced. However, most single-cell studies of infection quantify the expression of viral transcripts and proteins, rather than the amount of progeny virions released from infected cells. Here we overcome this limitation by simultaneously measuring transcription and progeny production from single influenza-virus-infected cells by embedding nucleotide barcodes in the viral genome. We find that viral transcription and progeny production are poorly correlated in single cells. The cells that transcribe the most viral mRNA do not produce the most viral progeny, and often represent aberrant infections that fail to express the influenza NS gene. However, only some of the discrepancy between transcription and progeny production can be explained by viral gene absence or mutations: there is also a wide range of progeny production among cells infected by complete unmutated virions. Overall, our results show that viral transcription is a relatively poor predictor of an infected cell’s contribution to the progeny population.
Silencing long-descending inter-enlargement propriospinal neurons improves hindlimb stepping after contusive spinal cord injuries
Authors: Shepard Courtney T , Brown Brandon L , Van Rijswijck Morgan A , Zalla Rachel M , Burke Darlene A , Morehouse Johnny R , Riegler Amberley S , Whittemore Scott R , Magnuson David SK
Published: September 2022

Spinal locomotor circuitry is comprised of rhythm generating centers, one for each limb, that are interconnected by local and long-distance propriospinal neurons thought to carry temporal information necessary for interlimb coordination and gait control. We showed previously that conditional silencing of the long ascending propriospinal neurons (LAPNs) that project from the lumbar to the cervical rhythmogenic centers (L1/L2 to C6), disrupts right-left alternation of both the forelimbs and hindlimbs without significantly disrupting other fundamental aspects of interlimb and speed-dependent coordination (Pocratsky et al., 2020). Subsequently, we showed that silencing the LAPNs after a moderate thoracic contusive spinal cord injury (SCI) resulted in better recovered locomotor function (Shepard et al., 2021). In this research advance, we focus on the descending equivalent to the LAPNs, the long descending propriospinal neurons (LDPNs) that have cell bodies at C6 and terminals at L2. We found that conditional silencing of the LDPNs in the intact adult rat resulted in disrupted alternation of each limb pair (forelimbs and hindlimbs) and after a thoracic contusion SCI significantly improved locomotor function. These observations lead us to speculate that the LAPNs and LDPNs have similar roles in the exchange of temporal information between the cervical and lumbar rhythm generating centers, but that the partial disruption of the pathway after SCI limits the independent function of the lumbar circuitry. Silencing the LAPNs or LDPNs effectively permits or frees-up the lumbar circuitry to function independently.
Mutations in CmVPS41 controlling resistance toCucumber Mosaic Virusdisplay specific subcellular localizations
Authors: Real Núria , Villar Irene , Serrano Irene , Guiu-Aragonés Cèlia , Martín-Hernández Ana Montserrat
Published: September 2022

Resistance toCucumber mosaic virus(CMV) in melon has been described in several exotic accessions. It is controlled by a recessive resistance gene,cmv1, which encodes a Vacuolar Protein Sorting 41 (CmVPS41).Cmv1prevents systemic infection by restricting the virus to the bundle sheath cells, preventing viral phloem entry. CmVPS41 from different resistant accessions carried two causal mutations, either a G85E change, found in Pat-81 and Freeman’s Cucumber, or L348R found inPI161375, cultivar Songwhan Charmi (SC). The analysis of the subcellular localization of CmVPS41 inN. benthamianahas revealed differential structures in resistant and susceptible accessions. Susceptible accessions showed nuclear and membrane spots and many transvacuolar strands, whereas the resistant accessions showed many intravacuolar invaginations. These specific structures colocalize with late endosomes. Artificial CmVPS41 carrying individual mutations causing resistance in the genetic background of CmVPS41 from the susceptible variety Piel de Sapo (PS), revealed that the structure most correlated with resistance was the absence of transvacuolar strands. Co-expression of CmVPS41 with the viral MPs, the determinant of virulence, did not change these localizations; however, infiltration of CmVPS41 from either SC or PS accessions in CMV-infectedN. benthamianaleaves showed a localization pattern closer to each other, with up to 30% cells showing some membrane spots in the CmVPS41SC and fewer transvacuolar strands (from a mean of 4 to 1-2) with CmVPS41PS. Our results suggest that the distribution of CmVPS41PS in late endosomes includes transvacuolar strands that facilitate CMV infection and that CmVPS41 is re-localized during viral infection.
Defining a Nonribosomal Specificity Code for Design
Authors: Stanišić Aleksa , Svensson Carl-Magnus , Ettelt Ulrich , Kries Hajo
Published: September 2022

Nonribosomal peptide synthetases (NRPSs) assemble bioactive peptides from an enormous repertoire of building blocks. How binding pocket residues of the nonribosomal adenylation domain, the so-called specificity code, determine which building block becomes incorporated has been a landmark discovery in NRPS enzymology. While specificity codes enable the prediction of substrate specificity from protein sequence, design strategies based on rewriting the specificity code have been limited in scope. An important reason for failed NRPS design has been that multispecificity has not been considered, for a lack of suitable assay formats. Here, we employ a multiplexed hydroxamate specificity assay (HAMA) to determine substrate profiles for mutant libraries of A-domain in the termination module the SrfAC of surfactin synthetase. A generalist version of SrfAC is developed and the functional flexibility of the adenylation reaction is probed by fully randomizing 15 residues in and around the active site. We identify mutations with profound impact on substrate selectivity and thus reveal a remarkable evolvability of A-domains. Statistical analysis of the specificity divergence caused by point mutations has determined the impact of each code position on specificity, which will serve as a roadmap for NRPS engineering. The shortness of evolutionary pathways between NRPS specificities explains the rich natural substrate scope and suggests directed evolution guided by A-domain promiscuity as a promising strategy.
Safe, effective, and inexpensive clearance of mycoplasma contamination from cultures of apicomplexan parasites with Sparfloxacin
Authors: Malave-Ramos Darlene R. , Kennedy Kit , Key Melanie N. , Dou Zhicheng , Kafsack Björn F.C.
Published: September 2022

Most commercial products cannot be used for clearance of mycoplasma contamination from cultures of apicomplexan parasites due to the parasites’ dependence on the apicoplast, an essential organelle with DNA replication and translation machinery of cyanobacterial origin. The lone exception, Mycoplasma Removal Agent (MRA), is relatively expensive and some mycoplasma strains have shown resistance to clearance with MRA. Here, we report that the fluoroquinolone antibiotic Sparfloxacin is a safe, effective, and inexpensive alternative for treatment of mycoplasma contamination in cultures of apicomplexan parasites. Sparfloxacin cleared both MRA- sensitive and MRA-resistant mycoplasma species from P. falciparum cultures at 1 and 4 μg/mL, respectively. We show that cultures of three different apicomplexan parasites can be maintained at concentrations of Sparfloxacin required to clear mycoplasma without resulting in substantial deleterious effects on parasite growth. We also describe an alternative low-cost, in-house PCR assay for detecting mycoplasma. These findings will be useful to laboratories maintaining apicomplexan parasites in vitro, especially in low-resource environments, where the high cost of commercial products creates an economic barrier for detecting and eliminating mycoplasma from culture.
Gene editing in the nematode parasite Nippostrongylus brasiliensis using extracellular vesicles to deliver active Cas9/guide RNA complexes
Authors: Hagen Jana , Ghosh Subhanita , Sarkies Peter , Selkirk Murray E.
Published: September 2022

Despite recent advances, animal-parasitic nematodes have thus far been largely refractory to genetic manipulation. We describe here a new approach providing proof of principle that CRISPR/Cas9-mediated gene editing of parasitic nematodes is achievable using vesicular stomatitis virus glycoprotein-pseudotyped extracellular vesicles (EV) for the delivery of Cas9-synthetic guide RNA (RNP) complexes. We demonstrate that EV-delivered RNPs can be used to disrupt a secreted DNase II in Nippostrogylus brasiliensis. Introduction of a repair template encoding multiple stop codons led to measurable reduction in expression of the targeted gene. Altered transcripts corresponding to the edited locus were detected by RT-PCR, demonstrating that vesicles can access cells of tissues actively expressing the gene of interest. These data provide evidence that this technique can be employed for targeted gene editing in N. brasiliensis, making this species genetically tractable for the first time and providing a new platform for genetic analysis of parasitic nematodes.

Author Summary

Parasitic nematodes have a complex life cycle involving passage through a host organism, which makes them very difficult to manipulate genetically. Recently, a method for deleting, changing or replacing genes (gene editing) has been developed in other organisms which has revolutionised our ability to understand fine details of how these organisms work. It has generally not been possible to adapt this method to parasitic nematodes because delivery of the components is difficult, and this has proved to be a bottleneck in understanding how parasites develop, survive and interact with their host. We show here that the components for gene editing can be introduced into a widely used laboratory model of intestinal nematode infection by encapsulation in membrane-bound vesicles which have been modified to carry a protein which facilitates fusion of the vesicles with parasite cells and delivery of the contents. This resulted in accurate editing of a specific gene by deletion and repair, such that the amount of functional protein produced from that gene was reduced. This system should be applicable to all nematode species, and will facilitate understanding of their complex biology, in addition to defining new targets for control of infection.
Knockout of ykcB, a putative glycosyltransferase, leads to vancomycin resistance in Bacillus subtilis
Authors: Ishikawa Kazuya , Shirakawa Riko , Takano Daiki , Kosaki Tomoki , Furuta Kazuyuki , Kaito Chikara
Published: September 2022

Vancomycin resistance of gram-positive bacteria poses a serious health concern around the world. In this study, we searched for vancomycin-resistant mutants from a gene deletion library of a model gram-positive bacterium, Bacillus subtilis, to elucidate the mechanism of vancomycin resistance. We found that knockout of ykcB, a glycosyltransferase that is expected to utilize C55-P-glucose to glycosylate cell surface components, caused vancomycin resistance in B. subtilis. Knockout of ykcB altered the susceptibility to multiple antibiotics, including sensitization to β-lactams, and increased the pathogenicity to silkworms. Furthermore, the ykcB-knockout mutant had: i) an increased content of diglucosyl diacylglycerol, a glycolipid that shares a precursor with C55-P-glucose, ii) a decreased amount of lipoteichoic acid, and iii) decreased biofilm formation ability. These phenotypes and vancomycin resistance were abolished by knockout of ykcC, a ykcB-operon partner involved in C55-P-glucose synthesis. Overexpression of ykcC enhanced vancomycin resistance in both wild-type B. subtilis and the ykcB-knockout mutant. These findings suggest that ykcB deficiency induces structural changes of cell surface molecules depending on the ykcC function, leading to resistance to vancomycin, decreased biofilm formation ability, and increased pathogenicity to silkworms.

IMPORTANCE

Although vancomycin is effective against gram-positive bacteria, vancomycin-resistant bacteria is a major public health concern. While the vancomycin resistance mechanisms of clinically important bacteria such as Staphylococcus aureus, Enterococcus faecium, and Streptococcus pneumoniae are well-studied, they remain unclear in other gram-positive bacteria. In the present study, we searched for vancomycin-resistant mutants from a gene deletion library of a model gram-positive bacterium, Bacillus subtilis, and found that knockout of a putative glycosyltransferase, ykcB, caused vancomycin resistance in B. subtilis. Notably, unlike the previously reported vancomycin-resistant bacterial strains, ykcB-deficient B. subtilis exhibited increased virulence while maintaining its growth rate. Our results broaden the fundamental understanding of vancomycin-resistance mechanisms in gram-positive bacteria.
Impact of reinfection with SARS-CoV-2 Omicron variants in previously infected hamsters
Authors: Shiwa-Sudo Nozomi , Sakai Yusuke , Iwata-Yoshikawa Naoko , Watanabe Shinji , Yamada Souichi , Kuroda Yudai , Yamamoto Tsukasa , Shirakura Masayuki , Fujisaki Seiichiro , Miyazaki Kaya , Miura Hideka , Nagata Shiho , Fukushi Shuetsu , Maeda Ken , Hasegawa Hideki , Suzuki Tadaki , Nagata Noriyo
Published: September 2022

The diversity of SARS-CoV-2 mutations raises the possibility of reinfection of individuals previously infected with earlier variants, and this risk is further increased by the emergence of the B.1.1.529 Omicron variant. In this study, we used anin vivo, hamster infection model to assess the potential for individuals previously infected with SARS-CoV-2 to be reinfected with Omicron variant and we also investigated the pathology associated with such infections. Initially, Syrian hamsters were inoculated with a lineage A, B.1.1.7, B.1.351, B.1.617.2 or a subvariant of Omicron, BA.1 strain and then reinfected with the BA.1 strain 5 weeks later. Subsequently, the impact of reinfection with Omicron subvariants (BA.1 and BA.2) in individuals previously infected with the BA.1 strain was examined. Although viral infection and replication were suppressed in both the upper and lower airways, following reinfection, virus-associated RNA was detected in the airways of most hamsters. Viral replication was more strongly suppressed in the lower respiratory tract than in the upper respiratory tract. Consistent amino acid substitutions were observed in the upper respiratory tract of infected hamsters after primary infection with variant BA.1, whereas diverse mutations appeared in hamsters reinfected with the same variant. Histopathology showed no acute pneumonia or disease enhancement in any of the reinfection groups and, in addition, the expression of inflammatory cytokines and chemokines in the airways of reinfected animals was only mildly elevated. These findings are important for understanding the risk of reinfection with new variants of SARS-CoV-2.

IMPORTANCE

The emergence of SARS-CoV-2 variants and the widespread use of COVID-19 vaccines has resulted in individual differences in immune status against SARS-CoV-2. A decay in immunity over time and the emergence of variants that partially evade the immune response can also lead to reinfection. In this study, we demonstrated that, in hamsters, immunity acquired following primary infection with previous SARS-CoV-2 variants was effective in preventing the onset of pneumonia after reinfection with the Omicron variant. However, viral infection and multiplication in the upper respiratory tract were still observed after reinfection. We also showed that more diverse nonsynonymous mutations appeared in the upper respiratory tract of reinfected hamsters that had acquired immunity from primary infection. This hamster model reveals the within-host evolution of SARS-CoV-2 and its pathology after reinfection, and provides important information for countermeasures against diversifying SARS-CoV-2 variants.
Taxonomic and metagenomic analyses define the development of the microbiota in the chick
Authors: Bogomolnaya Lydia , Talamantes Marissa , Rocha Joana , Nagarajan Aravindh , Zhu Wenhan , Spiga Luisella , Winter Maria G. , Konganti Kranti , Adams L. Garry , Winter Sebastian , Andrews-Polymenis Helene
Published: September 2022

Chicks are ideal to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Taxonomic/metagenomic analyses captured the development of the chick microbiota in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm) during development. Taxonomic analysis suggests that colonization by the chicken microbiota takes place in several waves. The cecal microbiota stabilizes at day 12 post-hatch with prominent Gammaproteobacteria and Clostridiales. Introduction of S. Typhimurium at day 4 post-hatch disrupted the expected waves of intestinal colonization. Taxonomic and metagenomic shotgun sequencing analyses allowed us to identify species present in uninfected chicks. Untargeted metabolomics suggested different metabolic activities in infected chick microbiota. This analysis, and GS-MS on ingesta confirmed that lactic acid in cecal content coincides with the stable presence of Enterococci in STm infected chicks. Unique metabolites including 2-isopropylmalic acid, an intermediate in the biosynthesis of leucine, was present only in the cecal content of STm infected chicks. Metagenomic data suggested that the microbiota in STm infected chicks contained a higher abundance of genes, from STm itself, involved in branched chain amino acid synthesis. We generated a deletion mutant in ilvC (STM3909) encoding ketol-acid-reductoisomerase, a gene required for the production of L-isoleucine and L-valine. ΔilvC mutants are disadvantaged for growth during competitive infection with the wild type. Providing the ilvC gene in trans restored growth of the ΔilvC mutant. Our integrative approach identified biochemical pathways used by STm to establish a colonization niche in the chick intestine during development.

IMPORTANCE

Chicks are an ideal model to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Using taxonomic and metagenomic analyses we captured the development of the chick microbiota to 19 days post-hatch in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm). We show that normal development of the microbiota takes place in waves, and is altered in the presence of a pathogen. Metagenomics and metabolomics suggested that branched chain amino acid biosynthesis is especially important for Salmonella growth in the infected chick intestine. Salmonella mutants unable to make L-isoleucine and L-valine colonize the chick intestine poorly. Restoration of the pathway for biosynthesis of these amino acids restored the colonizing ability of Salmonella. Integration of multiple analyses allowed us to correctly identify biochemical pathways used by Salmonella to establish a niche for colonization in the chick intestine during development.
Adapting UK Biobank imaging for use in a routine memory clinic setting: the Oxford Brain Health Clinic
Authors: Griffanti Ludovica , Gillis Grace , O’Donoghue M. Clare , Blane Jasmine , Pretorius Pieter M. , Mitchell Robert , Aikin Nicola , Lindsay Karen , Campbell Jon , Semple Juliet , Alfaro-Almagro Fidel , Smith Stephen M. , Miller Karla L. , Martos Lola , Raymont Vanessa , Mackay Clare E.
Published: September 2022

The Oxford Brain Health Clinic (BHC) is a joint clinical-research service that provides memory clinic patients and clinicians access to high-quality assessments not routinely available, including brain MRI aligned with the UK Biobank imaging study (UKB).

In this work we present how we 1) adapted the UKB MRI acquisition protocol to be suitable for memory clinic patients, 2) modified the imaging analysis pipeline to extract measures that are in line with radiology reports and 3) compared measures from BHC patients to the largest brain MRI study in the world (ultimately 100,000 participants).

Adaptations of the UKB acquisition protocol for BHC patients include dividing the scan into core and optional sequences (i.e., additional imaging modalities) to improve patients’ tolerance for the MRI assessment. We adapted the UKB structural MRI analysis pipeline to take into account the characteristics of a memory clinic population (e.g., high amount of white matter hyperintensities and hippocampal atrophy). We then compared the imaging derived phenotypes (IDPs) extracted from the structural scans to visual ratings from radiology reports, non-imaging factors (age, cognition) and to reference distributions derived from UKB data.

Of the first 108 BHC attendees (August 2020-November 2021), 92.5% completed the clinical scans, 88.0% consented to use of data for research, and 48.1% completed at least one additional research sequence, demonstrating that the protocol is well tolerated. The high rates of consent to research makes this a unique real-world quality research dataset routinely captured in a clinical service. Modified tissue-type segmentation with lesion masking greatly improved grey matter volume estimation. CSF-masking marginally improved hippocampal segmentation. The IDPs were in line with radiology reports and showed significant associations with age and cognitive performance, in line with the literature. Due to the age difference between memory clinic patients of the BHC (age range 65-101 years, average 78.3 years) and UKB participants (44-82 years, average 64 years), additional scans on elderly healthy controls are needed to improve reference distributions. Current and future work aims to integrate automated quantitative measures in the radiology reports and evaluate their clinical utility.
Investigating the genotoxicity of occupational pesticide exposures in Arab countries: Protocol of a systematic review and meta-analysis
Authors: Sherif Moustafa , Makame Khadija Ramadhan , Östlundh Linda , Paulo Marilia Silva , Nemmar Abderrahim , Ali Bassam R. , Rifai Rami Al , Nagy Károly , Ádám Balázs
Published: September 2022

Background

Tens of millions of agricultural workers are directly exposed to pesticides through handling pesticide products, mostly in developing countries. Systematic data synthesis on the genotoxic consequences of such occupational exposures and their human health risks in agricultural settings is required in Arab countries. We aim to conduct a systematic review and, if possible, a meta-analysis to review published literature about the genotoxicity of occupational pesticide exposures in Arab countries, with the objectives of characterising the (1) prevalence rates of genotoxic pesticide exposures, (2) extent of genotoxic insults, (3) attributed risk factors, and (4) preventive measures against pesticide-induced genotoxic effects detectable by biomonitoring.

Methods

The research will follow the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) statement. A comprehensive search will be conducted in November 2022 in the electronic databases PubMed (NLM), EMBASE (Elsevier), Web of Science (Clarivate), Scopus (Elsevier), and Agricola in addition to WHO Index Medicus for the Eastern Mediterranean (IMEMR). The search will be performed without any restrictions for publication years. A filter for English and Arabic language will be applied.

The systematic search will include agricultural workers over the age of 18 years, located in Arabic speaking countries of the Middle East and North Africa (MENA) region, occupationally exposed to pesticides inducing genotoxic insult detectable by biomonitoring.

Records identified in the search will be imported into the systematic review tool Covidence for blinded screening and selection by two reviewers independently. The reviewers will then extract data and conduct risk of bias assessment using the Navigation Guide RoB tool and the RoB-SPEO tool. The results will be synthetized narratively in summary tables, and, if findings allow, meta-analysis, including subgroup and sensitivity analysis, will be conducted on the prevalence of genotoxic pesticide exposures, and on the effect size of risk factors. The systematic review methodology does not require ethics approval.

Discussion

The systematic review will consider various types of pesticide exposures and genotoxicity biomarker assays to determine prevalence and extent of such occupational genotoxic insults, the correlation between genetic damage and various risk factors, e.g. work conditions, types of pesticides, environmental exposure routes, and the applied preventive measures. The review will provide gap-filling information about genotoxic pesticide exposures of agricultural workers in the local context, as well as it will contribute to our general knowledge on pesticide genotoxicity.

Systematic review registration

PROSPERO registration number: CRD42022314453.
Depressive symptoms anticipate behavioral and emotional factors among older adults: A prospective cross-lagged panel design
Authors: Kazan Joseph , Gerlach Andrew R. , Mizuno Akiko , Andreescu Carmen , Aizenstein Howard J. , Ward Scott , Buente Kara J. , Stahl Sarah T.
Published: September 2022

This study examined the temporal relationship among depression, anxiety, insomnia, perceived stress, and physical activity in adults aged 60+ years with a history of major depressive disorder. We conducted a longitudinal study with 12 weeks of follow-up. Assessments consisted of phone or video interviews and included questionnaires evaluating depression, anxiety, insomnia, perceived stress, and physical activity. Our analytic approach consisted of a depression-focused cross-lagged panel model (CLPM) to examine week-to-week correlations among the five measures. The depression-focused CLPM identified statistically significant week-to-week self-predictive effects for each of the five measures. Higher depressive symptom burden was a strong predictor of increased stress, greater insomnia, and less physical activity the following week. No other cross-measure predictions were statistically significant. Our analytical approach clarifies the directional relationship among variables that typically co-occur with depression showing that higher depression symptom burden predisposes older adults to poor sleep, a reduced level of daytime activity, and a greater sense of stress. These findings support the need for longitudinal assessments and targeted interventions for reducing symptoms of depression in older adults.
Family planning uptake and its associated factors among women of reproductive age in Uganda: an insight from the Uganda Demographic and Health Survey 2016
Authors: Ochen Anthony Mark , Chi Primus Che
Published: September 2022

Despite the government efforts to reduce the high fertility levels and increase uptake of family planning services in Uganda, family planning use was still low at 30% which is the lowest in the East African region. This study was undertaken to determine the prevalence and factors associated with the uptake of family planning methods among women of reproductive age in Uganda. This is a community-based cross-sectional study that utilized secondary data from the Uganda Demographic and Health Survey (UDHS) of 2016. The survey data was downloaded from the Measure Demographic Health Survey website after data use permission was granted. Data was collected from a representative sample of women of the reproductive age group (15-49 years) from all the 15 regions in Uganda. A total of 19,088 eligible women were interviewed but interviews were completed with 18,506 women. Data analysis was performed using SPSS statistical software version 32.0 where univariable, bivariable, and multivariable analyses were conducted. The prevalence of family planning use was found to be 29.3% and that of modern contraceptive use was found to be 26.6%. Multivariable analysis showed higher odds of current family planning use among older women (40-44 years) (aOR=2.09, 95% CI: 1.40-3.12); women who had attained the secondary level of education (aOR=1.91, 95% CI: 1.32-2.76); those living in households with the highest wealth index (aOR=1.87, 95% CI: 1.29-2.72); and awareness of the availability of family planning methods (aOR=1.41, 95% CI: 1.17-1.72). In conclusion, the study found a low prevalence of current family planning use among women of reproductive age and this calls for more efforts toward the advancement of women’s education, awareness creation, designing policies to popularize use of FP among adolescents and young women, and socio-economic empowerment of women.