bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacterial diversity of two types of Wagashi, a traditional Beninese cheese, using High-Throughput Amplicon Sequencing
Authors: Komagbe Gwladys S. , Sessou Philippe , Farougou Souaïbou , Mahillon Jacques
Published: May 2022

Wagashi, also called Gassiréin the local Fulfulde language, is a traditional cheese produced from cow milk in Benin. For its preparation, milk is heated and coagulated with Calotropis procera extract. After coagulation, the heated curd obtained is drained, moulded and stained, or not, using Sorghum vulgare or Sorghum codatum panicles. It is the most commonly consumed dairy product as surrogate for meat or fish. In order to get better insights into the bacterial diversity of Wagashi, Illumina MiSeq amplicon sequencing targeting the V1-V2 region of the bacterial 16S rRNA gene was performed on two different Wagashi types (stained and not stained) from Benin. The results showed that the Lactobacillaceae (60%) and Streptococcaceae (38%), were the most abundant bacteria in the unstained cheese, whereas Streptococcaceae (89%) and Bacillaceae (10%) were the most prevalent in stained cheese. Moreover, at the species level, the microbial community structures of stained and unstained cheeses were significantly different. The main differentiating species were Lactobacillus bulgaricus, Streptococcus thermophilus, and Lactobacillus fermentum in unstained cheese, compared to Streptococcus infantarius, Aeromonas sp., Bacillus cereus, Bacillus subtilis and S. thermophilus in stained cheese. This work provides valuable insights into microbiology of cheese Wagashi and shows that the staining of this dairy product affects its bacterial composition. In particular, the presence of potential useful Lactobacilli and Streptococci in unstained cheese is to be further investigated for selecting functional bacteria for potential biotechnology applications. On the contrary, the presence of Bacilli in stained cheese needs additional study to detect potential foodborne strains or pathotypes.
Evaluation of Drug Activity Against Staphylococcal Biofilms – Settings of Conditions Leading to Reproducible and Robust Biofilm Formation in vitro
Authors: Diepoltová Adéla , Konečná Klára , Jandurek Ondřej , Nachtigal Petr
Published: May 2022

Staphylococcus aureus(SA)andepidermidis(SE) are the most common pathogens of the genus Staphylococcus, causing biofilm-associated infections. Bacteria in biofilms are difficult to eradicate due to their resistance and serve as a reservoir for recurring persistent infections. A variety of protocols for in vitro drug activity testing against biofilms has been introduced. However, there are often fundamental differences. In our pilot study, we developed optimal conditions for staphylococcal biofilm formation on plastic pegs in order to set a methodology for an evaluation of the antibiofilm activity of candidate molecules. The convenience of the plastic pegs lies in their removability from the lid for easy access to multiple equivalent biofilms, and in possibility of in situ detection and quantification by confocal laser microscopy. For the purpose of enhancement in staphylococcal biofilm formation, the impact of peg surface modification with 3 different coating materials was studied as well. An increase of biofilm biomass was evaluated by crystal violet staining method. The basic precondition for obtaining relevant and reproducible data regarding antibiofilm activity is the formation of robust biofilms with typical attributes such as the presence of a biofilm matrix. In our study, in vitro conditions revealed that we fully met the preconditions for the SA and methicillin-resistant SA strains. In conclusion, we demonstrated statistically significant enhancement of biofilm formation in all studied staphylococcal strains, including either strong biofilm producer phenotype (SA, methicillin-resistant SA) and weak biofilm producer phenotype (SE).

Supported by the SVV Project No. 260549 and by the Czech Science Foundation project No. 20-19638Y.
Bioinformatic Analysis for Iron-Uptake System of Campylobacter spp. in humans and chickens
Authors: Kiourkou Mariklairi , Ketley Julian , Barratt Natalie
Published: May 2022

Asymptomatic Campylobacter jejuni colonisation is highly prevalent in chickens, however, it’s a major cause of bacterial foodborne disease in humans. Iron is an essential co-factor in many physiological processes and Campylobacter strains employ several non-redundant iron acquisition systems for survival and colonization. The outer membrane receptors CfrA and CfrB are involved in iron acquisition fromcatecholamine siderophores and are required for colonisation of the chicken GI tract. In contrast, ChuAB are part of an uptake system, enabling the utilization of iron in haem and is not required for colonisation. This study aims to compare differences in the iron-uptake systems present in Campylobacter strains isolated from chickens or humans.

Analysis of Campylobacter jejuni/coli genome sequences in PubMLST (https://pubmlst.org/organisms/campylobacter-jejunicoli [https://pubmlst.org/organisms/campylobacter-jejunicoli]) added from the UK in 2018 reveals differences in sequence type (ST) and chuA, chuB, cfrA and cfrB between isolates from chicken (CI) or human (HI) sources. ST828 was the most common ST for the C. coliCI (45%) and ST827 (32%) for the HI. C. jejuniST5136 was the most common of the HI (10%) and CI (13%), ST50 (8%) for the HI and ST21 (7%) for the CI. >95% of isolates contained chuAand chuB, we also found the Chu system to be highly conserved. For cfrA81% of HI and 74% of CI contained the gene, and 92% of HI and 96% of CI harboured cfrB.<3% of all isolates had neither cfrAor cfrB, cfrBmore associated with CI than HI. This data analysis reveals potential gene targets towards vaccine development against Campylobacter strains.
Identification and characterisation of a Novel SXT/R391 ICE mobile genetic element isolated from an Irish wastewater environment
Authors: Ryan Michael P , Slattery Shannon , Pembroke J Tony
Published: May 2022

Human and animal pathogenic bacteria are constantly being released into the environment through human activity. Many of these organisms can harbour genes such as virulence genes, antibiotic resistance and heavy metal resistance genes that are inserted into plasmids, transposons and Integrating Conjugating elements (ICEs), leading to potential spread. Such spread can be detected among water and soil communities and in particular in wastewater treatment plants. This makes wastewater and treatment plants a potential reservoir for mobile genetic elements including SXT/R391 ICEs, commonly detected amongst enterobacterial genera. Many plasmid and ICE genomes have been detected serendipitously from clinical sources but few have been identified without selection. Here we examined a domestic wastewater treatment plant to identify, isolate and characterize SXT/R391 ICE’s without selection. Standard microbial replica plating in conjunction with ICE specific (conserved integrase gene) PCR techniques were employed to identify an SXT/R391 ICE MGE using a range of enterobactial selective media. A Novel SXT/R391 ICE MGE was identified from a wastewater Proteus mirabilisstrain. Whole genome sequencing using Ilumina sequencing technology revealed a novel 81 kb element which on annotation contained 75 open reading frames. The “hotspot regions”, which contain adaptive genes, encoded a novel bacteriophage defence mechanisms but lacked other selectable determinants. With the continuous arms race between bacteria and phage, bacteria have developed novel resistance mechanism systems that protect the bacteria from phage. Such systems may be key adaptive mechanisms harboured by ICEs particularly in wastewater systems which will contain large phage populations.
Controlling the lytic switch; can m6A-modified RNA be used as an Anti-Viral Target?
Authors: Barker Amy , Fullenkamp Chris , Roder Konstanin , Pasquali Samuela , Schneekloth Jay , Whitehouse Adrian
Published: May 2022

KSHV has a biphasic life cycle encompassing a latent state and lytic replication. The KSHV replication and transcription activator viral protein, encoded from open reading frame 50 (ORF50), is the key viral protein which drives the switch between the latent and lytic phases (Guito and Lukac, 2012). We have recently demonstrated that KSHV manipulates the host cell N6-methyl adenosine (m6A) RNA modification pathway to enhance viral gene expression. Specifically, we have shown that the KSHV ORF50 transcript is m6A methylated, allowing the recruitment of the m6A reader protein, Staphylococcal nuclease domain-containing protein 1 (SND1), resulting in the stabilisation of the ORF50 transcript and efficient KSHV lytic replication (Baquero-Perez et al. 2019).

Further analysis of the m6A modified site with the ORF50 transcript has identified an RNA stem-loop, termed ORF50-1, which is a m6A-modified 43-mer, essential for SND-1 binding, thought to occur in a secondary structure/ sequence-dependent manner.

Generating in silico 3D structures of the ORF50-1 RNA in its native ‘N’ and m6A-modified ‘M’ form confirms that the presence of the m6A-modification has repercussions in the lower part of the stem-loop and predicts a different secondary structure(collab. Pasquale and Roeder).

Due to the obvious structural differences anticipated, RNA-binding ligands have been identified using Small Molecule Microarrays (SMMS) (collab. Fullenkamp and Schneekloth). By investigating these ligands in biophysicalexperiments, we have verified RNA-binding and optimised cell-based assays to assess anti-viral properties. It is hoped these experiments will highlight the importance of A versus m6A within the lytic phase of KSHV’s lifecycle.
Development of a lentivirus-mediated gene therapy targeting HIV-1 RNA to eliminate HIV-1-infected cells
Authors: Buckingham Amanda , Ho Sophia , Mok Hoi-Ping , Ingemarsdotter Carin , Lever Andrew
Published: May 2022

Only two patients have ever been cured of HIV-1. The latent HIV-1 reservoir is the major roadblock to this and necessitates lifelong therapy. In the ‘shock and kill’ approach to eliminate cells harbouring dormant virus the latency reversing agent (LRA) vorinostat increased HIV-1 RNA levels, but this failed to enable a reduction in reservoir size by immune- or virus-mediated cytotoxicity. To leverage LRAs’ ability to heighten HIV-1 transcription, we are developing a ‘kill’ strategy that hijacks the HIV-1 splicing process with a therapeutic trans-splicing RNA, encoding an incomplete Herpes simplex virus thymidine kinase (HSV-tk) that gains functionality by trans-splicing onto HIV-1 tat pre-mRNA. HSV-tk activates the exogenous prodrug ganciclovir for selective killing of HIV-1-infected cells. Following proof-of-principle transfection studies, therapeutic constructs were engineeredfor lentivirus-mediated delivery to HIV-infected cells in vitro. We optimized lentiviral production for high infectious titer (>106 TU/mL) and low vector plasmid carryover (<1 copy/cell). In a tissue culture model of HIV-1 infection we confirmed lentiviral delivery of therapeutic (and control) vectors. Successful trans-splicing of the HSV-tk RNA onto HIV-1 RNA in cells co-transduced with HIV-1 and therapeutic vector at an MOI as low as 4 was confirmed by sequencing. In MTT assays the most potent therapeutic vector killed approximately 80% of HIV-1-expressing cells. Next-generation vectors are being evaluated for enhanced therapeutic potential and improved HIV-1-targeting RNA expression. The lead candidate culminating from this work will be assessed for selective killing of HIV-1-infected cells both productively infected and with virus reactivated from latency.
Failing to control Maedi-Visna
Authors: Jones Scott , Lovatt Fiona , Davies Peers , Dunham Stephen , Tarlinton Rachael
Published: May 2022

Maedi-Visna is a lentivirus of sheep that causes lung disease and chronic wasting. It has been designated an “Iceberg disease” by the UK sheep industry levy board with a very large burden of subclinical disease that is often not apparent until losses in an individual flock become catastrophic. Disease prevalence in the UK is thought to have doubled in the last 10 years, however farmer and veterinary awareness of the disease is poor. There is no vaccine and treatment is not cost effective, meaning that the only realistic control option is culling of affected animals.

Current testing protocols use MV gag protein ELISAs. A long lag time between infection and antibody production means that many animals are missed on flock screening and repeated rounds of testing over a period of years are necessary to remove all infected animals. Preliminary testing of flocks that have attempted eradication indicates that those that do not keep testing until all animals are negative fail to eliminate the disease and that prevalence rates can even increase substantially in these flocks. The viruses extreme variability confounded attempts to develop a qPCR capable of detecting all variants, indeed deep sequencing was required to establish which strains of virus are currently present in UK sheep as there has been substantial genetic drift since the last sequencing studies (performed more than 20 years ago). More promisingly virus was detectable in nasal swabs of experimental animals at least offering sampling methods that can be done by farmers themselves.
Novosphingobium percolationis sp. nov. and Novosphingobium huizhouense sp. nov., isolated from landfill leachate of a domestic waste treatment plant
Authors: He Xiaoling , Lu Huibin , Hu Wenzhe , Deng Tongchu , Gong Xiaofan , Yang Xunan , Song Da , He Mei , Xu Meiying
Published: May 2022

Two strains designated as c1T and c7T, were isolated from the landfill leachate of a domestic waste treatment plant in Huizhou City, Guangdong Province, PR China. The cells of both strains were aerobic, rod-shaped, non-motile and formed yellow colonies on Reasoner’s 2A agar plates. Strain c1T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 7.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Strain c7T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 6.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Phylogenetic analyses revealed that strains c1T and c7T belong to the genus

Novosphingobium

. The 16S rRNA gene sequence similarities of strains c1T and c7T to the type strains of

Novosphingobium

species were 94.5–98.2 % and 94.3–99.1 %, respectively. The calculated pairwise average nucleotide identity values among strains c1T, c7T and the reference strains were in the range of 75.2–85.9 % and the calculated pairwise average amino acid identity values among strains c1T, c7T and reference strains were in the range of 72.0–88.3 %. Their major respiratory quinone was Q-10, and the major cellular fatty acids were C18 : 1
 ω7c, C18 : 0, C16 : 1
 ω7c, C16 : 0 and C14 : 0 2OH. The major polar lipids of strains c1T and c7T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, unidentified lipids and unidentified phospholipid. Based on phenotypic, chemotaxonomic, phylogenetic and genomic results from this study, strains c1T and c7T should represent two independent novel species of

Novosphingobium

, for which the names Novosphingobium percolationis sp. nov. (type strain c1T=GDMCC 1.2555T=KCTC 82826T) and Novosphingobium huizhouense sp. nov. (type strain c7T=GDMCC 1.2556T=KCTC 82827T) are proposed. The gene function annotation results of strains c1T and c7T suggest that they could play an important role in the degradation of organic pollutants.
Generalizable Long COVID Subtypes: Findings from the NIH N3C and RECOVER Programs
Authors: Reese Justin T. , Blau Hannah , Bergquist Timothy , Loomba Johanna J. , Callahan Tiffany , Laraway Bryan , Antonescu Corneliu , Casiraghi Elena , Coleman Ben , Gargano Michael , Wilkins Kenneth J. , Cappelletti Luca , Fontana Tommaso , Ammar Nariman , Antony Blessy , Murali T. M. , Karlebach Guy , McMurry Julie A , Williams Andrew , Moffitt Richard , Banerjee Jineta , Solomonides Anthony E. , Davis Hannah , Kostka Kristin , Valentini Giorgio , Sahner David , Chute Christopher G. , Madlock-Brown Charisse , Haendel Melissa A , Robinson Peter N. ,   the RECOVER Consortium
Published: May 2022

Accurate stratification of patients with post-acute sequelae of SARS-CoV-2 infection (PASC, or long COVID) would allow precision clinical management strategies. However, the natural history of long COVID is incompletely understood and characterized by an extremely wide range of manifestations that are difficult to analyze computationally. In addition, the generalizability of machine learning classification of COVID-19 clinical outcomes has rarely been tested. We present a method for computationally modeling PASC phenotype data based on electronic healthcare records (EHRs) and for assessing pairwise phenotypic similarity between patients using semantic similarity. Our approach defines a nonlinear similarity function that maps from a feature space of phenotypic abnormalities to a matrix of pairwise patient similarity that can be clustered using unsupervised machine learning procedures. Using k-means clustering of this similarity matrix, we found six distinct clusters of PASC patients, each with distinct profiles of phenotypic abnormalities. There was a significant association of cluster membership with a range of pre-existing conditions and with measures of severity during acute COVID-19. Two of the clusters were associated with severe manifestations and displayed increased mortality. We assigned new patients from other healthcare centers to one of the six clusters on the basis of maximum semantic similarity to the original patients. We show that the identified clusters were generalizable across different hospital systems and that the increased mortality rate was consistently observed in two of the clusters. Semantic phenotypic clustering can provide a foundation for assigning patients to stratified subgroups for natural history or therapy studies on PASC.
Exploring county-level spatio-temporal patterns in opioid overdose related emergency department visits
Authors: Acharya Angeela , Izquierdo Alyssa M , Gonçalves Stefanie F , Bates Rebecca A , Taxman Faye S , Slawski Martin P , Rangwala Huzefa S , Sikdar Siddhartha
Published: May 2022

Opioid overdoses within the United States continue to rise and have been negatively impacting the social and economic status of the country. In order to effectively allocate resources and identify policy solutions to reduce the number of overdoses, it is important to understand the geographical differences in opioid overdose rates and their causes. In this study, we utilized data on emergency department opioid overdose (EDOOD) visits to explore the county-level spatio-temporal distribution of opioid overdose rates within the state of Virginia and their association with aggregate socio-ecological factors. The analyses were performed using a combination of techniques including Moran’s I and multilevel modeling. Using data from 2016-2021, we found that Virginia counties had notable differences in their EDOOD visit rates with significant neighborhood-level associations: many counties in the southwestern region were consistently identified as the hotspots (areas with a higher concentration of EDOOD visits) whereas many counties in the northern region were consistently identified as the coldspots (areas with a lower concentration of EDOOD visits). In most Virginia counties, EDOOD visit rates declined from 2017 to 2018. In more recent years (since 2019), the visit rates showed an increasing trend. The multilevel modeling revealed that the change in clinical care factors (i.e., access to care and quality of care) and socio-economic factors (i.e., levels of education, employment, income, family and social support, and community safety) were significantly associated with the change in the EDOOD visit rates. The findings from this study have the potential to assist policymakers in proper resource planning thereby improving health outcomes.
In the Midst of a Pandemic, Introverts May Have a Mortality Advantage
Authors: Glei Dana A. , Weinstein Maxine
Published: May 2022

Extroverts may enjoy lower mortality than introverts under normal circumstances, but the relationship may be different during an airborne pandemic when social contact can be deadly. We used data for midlife Americans surveyed in 1995-96 with mortality follow-up through December 31, 2020 to investigate whether the association between extroversion and mortality changed during the COVID-19 pandemic. We hypothesized that excess mortality during the pandemic will be greater for extroverts than for introverts. Results were based on a Cox model estimating age-specific mortality controlling for sex, race/ethnicity, the period trend in mortality, and an additional indicator for the pandemic period (Mar-Dec 2020). We interacted extroversion with the pandemic indicator to test whether the relationship differed between prepandemic and pandemic periods. Prior to the pandemic, extroversion was associated with somewhat lower mortality (HR=0.93 per SD, 95% CI 0.88-0.97), but the relationship reversed during the pandemic: extroverted individuals appeared to suffer higher mortality than their introverted counterparts, although the effect was not significant (HR=1.20 per SD, 95% CI 0.93-1.54).

Extroversion was associated with greater pandemic-related excess mortality (HR=1.20/0.93=1.29 per SD, 95% CI 1.00-1.67). Compared with someone who scored at the mean level of extroversion, mortality rates prior to the pandemic were 10% lower for a person who was very extroverted (i.e., top 12% of the sample at Wave 1), while they were 12% higher for someone who was very introverted (i.e., 11th percentile). In contrast, mortality rates during the pandemic appeared to be higher for very extroverted individuals (HR=1.15, 95% CI 0.77-1.71) and lower for those who were very introverted (HR=0.70, 95% CI 0.43-1.14) although the difference was not significant because of limited statistical power. In sum, the slight mortality advantage enjoyed by extroverts prior to the pandemic disappeared during the first 10 months of the COVID-19 pandemic. It remains to be seen whether that pattern continued into 2021-22. We suspect that the mortality benefit of introversion during the pandemic is largely a result of reduced exposure to the risk of infection, but it may also derive in part from the ability of introverts to adapt more easily to reduced social interaction without engaging in self-destructive behavior (e.g., drug and alcohol abuse). Introverts have been training for a pandemic their whole lives.
Pattern, preferences, barriers, and correlates of self-reported physical activity in adults with borderline personality disorder: An online survey in western countries
Authors: St-Amour Samuel , Cailhol Lionel , Lapointe Josyanne , Ducasse Déborah , Landry Gabrielle , Bernard Paquito
Published: May 2022

Borderline personality disorder (BPD) is characterized by an instability of self-image, interpersonal relationships, and emotions and is highly comorbid with other disorders. Physical activity has shown great results in treating these disorders. Physical activity intervention should be built considering the preferences and barriers of the targeted individuals. However, to this day no study analyzed the preferences and barriers to physical activity in individuals with BPD, which is the goal of this study. We used an online survey to question 192 adults with a self-reported diagnosis of BPD from Canada, France, the United States, England, Switzerland, and New Zealand. Participants complete 607 minutes of physical activity weekly on average. They prefer walking (66.7%), biking (33.3%), aquatic activities (29.0%), and running (24.2%). Their main barriers to physical activity are having a friend over, having other engagements, and recovering from an injury. They also prefer doing individual supervised physical activity outside and in a long session of moderate intensity. Finally, a majority of participants are interested in receiving physical activity advice, but most did not. The professionals from whom they would prefer to receive advice are trainers, psychiatrists, physical therapists, and psychologists. These results are important to better tailor future physical activity interventions for adults with BPD.
The effects of reduced nicotine content cigarettes in smokers with mood or anxiety disorders: a double-blind randomized trial
Authors: Foulds Jonathan , Veldheer Susan , Pachas Gladys , Hrabovsky Shari , Hameed Ahmad , Allen Sophia I , Cather Corinne , Azzouz Nour , Yingst Jessica , Hammett Erin , Modesto Jennifer , Krebs Nicolle M , Lester Courtney , Trushin Neil , Reinhart Lisa , Wasserman Emily , Zhu Junjia , Liao Jason , Muscat Joshua E , Richie John P , Evins A Eden
Published: May 2022

BACKGROUND

The U.S. Food and Drug Administration and the government of New Zealand have proposed a reduction of the nicotine content in cigarettes to very low levels. This study examined the likely effects of this regulation in smokers with affective disorders.

METHODS

In a randomized controlled trial conducted at two sites (Penn State Hershey and Massachusetts General Hospital, Boston) 188 adult smokers with a current or lifetime anxiety or unipolar mood disorder, not planning to quit in the next 6 months, were randomly assigned to smoke either Usual Nicotine Content (UNC) (11.6 mg nicotine/cigarette) cigarettes, or Reduced Nicotine Content (RNC) cigarettes where the nicotine content per cigarette was progressively reduced to 0.2 mg in five steps over 18 weeks. Participants were then offered the choice to either receive assistance to quit smoking, receive free research cigarettes, or resume using their own cigarette brand during a 12-week follow-up period. Main outcomes were biomarkers of nicotine and toxicant exposure, smoking behavior and dependence and severity of psychiatric symptoms.

RESULTS

After switching to the lowest nicotine content cigarettes, compared to smokers in the UNC group, the RNC group had significantly lower plasma cotinine (metabolite of nicotine), urine NNAL (metabolite of NNK, a lung carcinogen), exhaled carbon-monoxide, cigarette consumption, and cigarette dependence. There were no significant effects on psychiatric symptoms. At the end of the 12-week treatment choice phase, those randomized to the RNC group were more likely to have quit smoking (18% RNC v 4% UNC, p=0.004).

CONCLUSION

Reducing nicotine content in cigarettes to very low levels reduces toxicant exposure and cigarette addiction and increases smoking cessation in smokers with mood and/or anxiety disorders, without worsening mental health.

Trial registration

TRN: NCT01928758, registered August 21, 2013
The effect of multigeneration history of suicidality on offspring’s neurodevelopment outcomes: evidence from the Adolescent Brain and Cognitive Development (ABCD) cohort
Authors: Wen Xue , Qu Diyang , Wu Guowei , Liu Dongyu , Wang Yuanyuan , Cui Zaixu , Zhang Xiaoqian , Chen Runsen
Published: May 2022

Background

Parent-child transmission of suicidal behaviors has been widely elucidated, while the three-generation family suicide risk paradigm remains to be explored. This longitudinal study aimed to examine the influences of family history of suicidality (FHoS) among two prior generations on offspring’s neurodevelopment.

Methods

We conducted a retrospective, longitudinal study using the Adolescent Brain Cognitive Development (ABCD) study data collected from 2016 to 2021. Participants were allocated into four groups according to their parents’ (Generation 1 [G1]) and grandparents’ (Generation 2 [G2]) history of suicidality (G1−G2−; G1+G2−; G1−/G2+; G1+/G2+). We estimated adjusted associations between FHoS and offspring’s suicide ideation (SI), psychopathology, impulsivity and brain cortical volumes while controlling for age, sex, parental education, household income and marital status.

Findings

A total of 11,875 children aged 9-10 years were observed from baseline to 3-year follow-up. Compared to G1-G2-, higher odds of SI were observed for G1-G2+ (OR=1·99, 95% CI [1·54-2·56]) and G1+G2+ (2·25 [1·46-3·47]) by child-report. Higher odds of SI were also observed for G1+G2- (1·54 [1·12-2·12]), G1-G2+ (2·57 [1·89-3·48]) and G1+G2+ (2·70 [1·60-4·56]) by caregiver-report. Higher odds for psychopathology were also observed (1·47 [1·11-1·96]; 3·33 [2·57-4·33]; 5·44 [3·42-8·66]), while higher family suicide risk was associated with high impulsivity (B=1·32 [0·48-2·17]; 2·24 [1·32-3·15]; 2·26 [0·47-4·05]). Offspring in G1+G2-had higher cortical volumes in 12 brain regions, including the bilateral insula, temporal regions and occipital regions, which were also significantly associated with their lifetime SI.

Discussion

A cumulative risk pattern of FHoS in two prior generations was found for offspring’s neurodevelopmental outcomes. Earlier preventive interventions are warranted to weaken the familial transmission of suicidal risk.
Segregation analysis of 17,425 population-based breast cancer families: evidence for genetic susceptibility and risk prediction
Authors: Li Shuai , MacInnis Robert J. , Lee Andrew , Nguyen-Dumont Tu , Dorling Leila , Carvalho Sara , Dite Gillian S. , Shah Mitul , Luccarini Craig , Wang Qin , Milne Roger L. , Jenkins Mark A. , Giles Graham G. , Dunning Alison M. , Pharoah Paul D.P. , Southey Melissa C. , Easton Douglas F. , Hopper John L. , Antoniou Antonis C.
Published: May 2022

Rare pathogenic variants in known breast cancer susceptibility genes and known common susceptibility variants do not fully explain the familial aggregation of breast cancer. To investigate plausible genetic models for the residual familial aggregation, we studied 17,425 families ascertained through population-based probands, 86% of whom were screened for pathogenic variants in BRCA1, BRCA2, PALB2, CHEK2, ATM and TP53 using gene-panel sequencing. We conducted complex segregation analyses and fitted genetic models in which breast cancer incidence depended on the effects of pathogenic variants in known susceptibility genes and other unidentified major genes, and a normally distributed polygenic component. The proportion of familial variance explained by BRCA1, BRCA2, PALB2, CHEK2, ATM and TP53 was 46% at age 20-29 years and decreased steadily with age thereafter. After allowing for these genes, the best fitting model for the residual familial variance included a recessively inherited risk component with a combined genotype frequency of 1.7% (95% CI: 0.3-5.4%) and a penetrance to age 80 years of 69% (95% CI: 38-95%) for homozygotes, and a polygenic variance of 1.27 (95% CI: 0.94-1.65) which did not vary with age. The proportion of the residual familial variance explained by the recessive risk component was 40% at age 20-29 years and decreased with age thereafter. The model predicted age-specific familial relative risks consistent with those observed by large epidemiological studies. The findings have implications for strategies to identify new breast cancer susceptibility genes and improve breast cancer risk prediction, especially at a young age.
Omicron reactive multi protein specific CD4 T cells defines cellular immune response induced by inactivated virus vaccines
Authors: Lim Joey Ming Er , Hang Shou Kit , Hariharaputran Smrithi , Chia Adeline , Tan Nicole , Lee Eng Sing , Chng Edwin , Lim Poh Lian , Young Barnaby , Lye David Chien , Le Bert Nina , Bertoletti Antonio , Tan Anthony T
Published: May 2022

Unlike mRNA vaccines based only on the Spike protein, inactivated SARS-CoV-2 vaccines should induce a diversified T cell response recognizing distinct structural proteins. Here we performed a comparative analysis of SARS-CoV-2 specific T cells in healthy individuals following vaccination with inactivated SARS-CoV-2 or mRNA vaccines. Relative to Spike mRNA vaccination, inactivated vaccines elicited a lower magnitude of Spike-specific T cells, but the combined Membrane, Nucleoprotein and Spike-specific T cell response was quantitatively comparable to the sole Spike T cell response induced by mRNA vaccines, and they efficiently tolerate the mutations characterizing the Omicron lineage. However, this multi-protein specific T cell response was not mediated by a coordinated CD4 and CD8 T cell expansion but by selected priming of CD4 T cells. These findings can help in defining the role of CD4 and CD8 T cells in the efficacy of the different vaccines to control severe COVID-19 after Omicron infection.
Adaptation delay causes a burst of mutations in bacteria responding to oxidative stress
Authors: Lagage Valentine , Chen Victor , Uphoff Stephan
Published: May 2022

Understanding the interplay between phenotypic plasticity and genetic adaptation is a long-standing focus of evolutionary biology. In bacteria, the oxidative stress response limits the formation of mutagenic reactive oxygen species (ROS) under diverse stress conditions. This suggests that the dynamics of the oxidative stress response are closely tied to the timing of the mutation supply that fuels genetic adaptation to stress. Here, we explored how mutation rates change in real-time in Escherichia coli cells during continuous hydrogen peroxide treatment in microfluidic channels. By visualising nascent DNA replication errors, we uncovered that sudden oxidative stress causes a burst of mutations. We developed a range of single-molecule and single-cell microscopy assays to determine how these mutation dynamics arise from phenotypic adaptation mechanisms. Signalling of peroxide stress by the transcription factor OxyR rapidly induces ROS scavenging enzymes. However, an adaptation delay leaves cells vulnerable to the mutagenic and toxic effects of hydroxyl radicals generated by the Fenton reaction. Resulting DNA damage is counteracted by a spike in DNA repair activities during the adaptation delay. Prior stress exposure or constitutive OxyR induction allowed cells to avoid the burst of mutations. Similar observations for alkylation stress show that mutation bursts are a general phenomenon associated with adaptation delays.
Phylogenomic diversity elucidates mechanistic insights into Lyme borreliae host association
Authors: Combs Matthew , Marcinkiewicz Ashley L. , Dupuis Alan P. , Davis April D. , Lederman Patricia , Nowak Tristan A. , Stout Jessica L. , Strle Klemen , Fingerle Volker , Margos Gabriele , Ciota Alexander T. , Diuk-Wasser Maria A. , Kolokotronis Sergios-Orestis , Lin Yi-Pin
Published: May 2022

Host association– the selective adaptation of pathogens to specific host species – evolves through constant interactions between host and pathogens, leaving a lot yet to be discovered on immunological mechanisms and genomic determinants. The causative agents of Lyme disease (LD) are spirochete bacteria composed of multiple species of the Borrelia burgdorferi sensu lato complex, including B. burgdorferi (Bb), the main LD pathogen in North America – a useful model for the study of mechanisms underlying host-pathogen association. Host adaptation requires pathogens’ ability to evade host immune responses, such as complement, the first-line innate immune defense mechanism. We tested the hypothesis that different host adapted phenotypes among Bb strains are linked to polymorphic loci that confer complement evasion traits in a host-specific manner. We first examined the survivability of 20 Bb strains in sera in vitro and/or bloodstream and tissues in vivo from rodent and avian LD models. Three groups of complement-dependent host association phenotypes emerged. We analyzed complement-evasion genes, identified a priori among all strains and sequenced and compared genomes for individual strains representing each phenotype. The evolutionary history of ospC loci is correlated with host-specific complement-evasion phenotypes, while comparative genomics suggests several gene families and loci are potentially involved in host association. This multidisciplinary work provides novel insights into the functional evolution of host adapted phenotypes, building a foundation for further investigation of the immunological and genomic determinants of host association.

IMPORTANCE

Host association is the phenotype that is commonly found in many pathogens that preferential survive in particular hosts. The Lyme disease (LD) causing agent, B. burgdorferi (Bb), is an ideal model to study host association, as Bb is mainly maintained in nature through rodent and avian hosts. A widespread yet untested concept posits that host association in Bb strains is linked to Bb functional genetic variation conferring evasion to complement, an innate defense mechanism in vertebrate sera. Here, we tested this concept by grouping 20 Bb strains into three complement-dependent host association phenotypes based on their survivability in sera and/or bloodstream and distal tissues in rodent and avian LD models. Phylogenomic analysis of these strains further correlated several gene families and loci, including ospC, with host-specific complement-evasion phenotypes. Such multifaceted studies thus pave the road to further identify the determinants of host association, providing mechanistic insights into host-pathogen interaction.
INSERT-seq enables high resolution mapping of genomically integrated DNA using nanopore sequencing
Authors: Ivančić Dimitrije , Mir-Pedrol Júlia , Jaraba-Wallace Jessica , Rafel Núria , Sanchez-Mejias Avencia , Güell Marc
Published: May 2022

Comprehensive characterization of genome engineering with viral vectors, transposons, CRISPR/Cas mediated DNA integration and other DNA editors remains relevant for their development and safe use in human gene therapy. Currently, described methods for measuring DNA integration in edited cells rely on short read based technologies. Due to the repetitive nature of the human genome, short read based methods can potentially overlook insertion events in repetitive regions. We modelled the impact of read length in resolving insertion sites, which suggested a significant drop in insertion site detection with shorter read length. Based on that, we developed a method that combines targeted amplification of integrated DNA, UMI-based correction of PCR bias and Oxford Nanopore long-read sequencing for robust analysis of DNA integration in a genome. This method, called INSERT-seq, is capable of detecting events occurring at a frequency of up to 0.1%. INSERT-seq presents a complete handling of all insertions independently of repeat size. The experimental pipeline improves the number mappable insertions at repetitive regions by 7.3% and repeats larger than the long read sequencing size are processed computationally to perform a peak calling in a repeat database. INSERT-seq is a simple, cheap and robust method to quantitatively characterise DNA integration in diverse ex-vivo and in-vivo samples.
Increasing evenness and stability in synthetic microbial consortia
Authors: Choudhary Ruhi , Mahadevan Radhakrishnan
Published: May 2022

Construction of successful synthetic microbial consortia will harbour a new era in the field of agriculture, bioremediation, and human health. Engineering communities is a complex, multi-dimensional problem with several considerations ranging from the choice of consortia members and spatial factors to genetic circuit performances. There has been a growing number of computational strategies to aid in synthetic microbial consortia design, but a framework to optimize communities for two essential properties, evenness and stability, is missing. We investigated how the structure of different social interactions (cooperation, competition, and predation) in quorum-sensing based circuits impacts robustness of synthetic microbial communities and specifically affected evenness and stability. Our proposed work predicts engineering targets and computes their operating ranges to maximize the probability of synthetic microbial consortia to have high evenness and high stability. Our exhaustive pipeline for rapid and thorough analysis of large and complex parametric spaces further allowed us to dissect the relationship between evenness and stability for different social interactions. Our results showed that in cooperation, the speed at which species stabilizes is unrelated to evenness, however the region of stability increases with evenness. The opposite effect was noted for competition, where evenness and stable regions are negatively correlated. In both competition and predation, the system takes significantly longer to stabilize following a perturbation in uneven microbial conditions. We believe our study takes us one step closer to resolving the pivotal debate of evenness-stability relationship in ecology and has contributed to computational design of synthetic microbial communities by optimizing for previously unaddressed properties allowing for more accurate and streamlined ecological engineering.
Increased microtubule lattice spacing correlates with selective binding of kinesin-1 in cells
Authors: de Jager Leanne , Jansen Klara I. , Kapitein Lukas C. , Förster Friedrich , Howes Stuart C.
Published: May 2022

Within the cell cargo is transported via motor proteins walking along microtubules. The affinity of motor proteins for microtubules is controlled by various layers of regulation like tubulin isoforms, post- translational modifications and microtubule associated proteins. Recently, the conformation of the microtubule lattice has also emerged as a potential regulatory factor, but to what extent it acts as an additional layer of regulation has remained unclear. In this study, we used cryo-correlative light and electron microscopy to study microtubule lattices inside cells. We find that, while most microtubules have a compacted lattice (∼41 Å), a significant proportion of the microtubule cores have expanded lattice spacings and that these lattice spacings could be modulated by the microtubule stabilizing drug Taxol. Furthermore, kinesin-1 predominantly binds microtubules with a more expanded lattice spacing (∼41.6 Å). The different lattice spacings present in the cell can thus act as an additional factor that modulates the binding of motor proteins to specific microtubule subsets.
rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly
Authors: Sekulski Kamil , Cruz Victor Emmanuel , Weirich Christine S. , Erzberger Jan P.
Published: May 2022

Biogenesis of the large ribosomal (60S) subunit involves the assembly of three rRNAs and 46 proteins, a process requiring approximately 70 ribosome biogenesis factors (RBFs) that bind and release the pre-60S at specific steps along the assembly pathway. The methyltransferase Spb1 and the K-loop GTPase Nog2 are essential RBFs that engage the rRNA A-loop during sequential steps in 60S maturation. Spb1 methylates the A-loop nucleotide G2922 and a catalytically deficient mutant strain (spb1D52A) has a severe 60S biogenesis defect. However, the assembly function of this modification is currently unknown. Here, we present cryo-EM reconstructions that reveal that unmethylated G2922 leads to the premature activation of Nog2 GTPase activity and capture a Nog2-GDP-AlF4- transition state structure that shows the direct involvement of unmodified G2922 in Nog2 GTPase activation. Intragenic and dosage suppressors indicate that the biogenesis defect in the spb1D52A strain is caused by reduced initial recruitment of Nog2 to early nucleoplasmic 60S intermediates. We propose that G2922 methylation levels regulate Nog2 stability on the pre-60S near the nucleolar/nucleoplasmic phase boundary, forming a kinetic checkpoint to regulate 60S production. Because multiple K-loop GTPases are involved in the assembly of ribosomes and other RNPs, our findings provide a template to study the role of RNA trans factors in modulating the regulatory functions of this important family of enzymes.
Post-mitotic centriole disengagement and maturation leads to centrosome amplification in polyploid trophoblast giant cells
Authors: Buss Garrison , Stratton Miranda B. , Milenkovic Ljiljana , Stearns Tim
Published: May 2022

DNA replication is normally coupled with centriole duplication in the cell cycle. Trophoblast giant cells (TGCs) of the placenta undergo endocycles resulting in polyploidy but their centriole state is not known. We used a cell culture model for TGC differentiation to examine centriole and centrosome number and properties. Prior to differentiation, trophoblast stem cells (TSCs) have either two centrioles before duplication, or four centrioles after. We find that average nuclear area increases approximately 8-fold over differentiation, but most TGCs do not have more than four centrioles. However, these centrioles become disengaged, acquire centrosome proteins, and can nucleate microtubules. In addition, some TGCs undergo further duplication and disengagement of centrioles, resulting in substantially higher numbers. Live imaging revealed that disengagement and separation are centriole autonomous and can occur asynchronously. Centriole amplification, when present, occurs by the standard mechanism of one centriole generating one procentriole. PLK4 inihibition blocks centriole formation in differentiating TGCs but does not affect endocycle progression. In summary, centrioles in TGC endocycles undergo disengagement and conversion to centrosomes. This increases centrosome number, but to a limited extent compared with DNA reduplication.
Targeted directional kilobase sequence insertion by combining prime editing with recombinases or integrases
Authors: Jillette Nathaniel , Zhu Jacqueline Jufen , Cheng Albert Wu
Published: May 2022

Targeted insertion of exogenous sequences to genomes is useful for therapeutics and biological research. While CRISPR/Cas technologies have been very efficient in gene knockouts by double-strand breaks (DSBs) followed by indel formation through non-homologous end-joining (NHEJ) repair pathway, the precise introduction of new sequences mainly rely on inefficient homology directed repair (HDR) pathways following Cas9-induced DSBs and are restricted to dividing cells. The recent invention of Prime Editing allows short sequences to be precisely inserted at target sites without DSBs. Here, we combine Prime Editing and sequence-specific recombinases and integrases to insert kilobase sequences directionally at target sites. This technique, called PRIMAS for Prime editing, Recombinase, Integrase-mediated Addition of Sequence, will expand our genome editing toolbox for targeted insertion of long sequences up to kilobases and beyond.
The exocyst complex is an essential component of the mammalian constitutive secretory pathway
Authors: Pereira Conceição , Stalder Danièle , Anderson Georgina , Shun-Shion Amber S. , Houghton Jack , Antrobus Robin , Chapman Michael A. , Fazakerley Daniel J. , Gershlick David C.
Published: May 2022

Secreted proteins fulfil a vast array of different functions, including adaptive immunity, cell signalling and extracellular matrix remodelling. In the trans-Golgi network, proteins destined for constitutive secretion are sorted into post-Golgi carriers which fuse with the plasma membrane to deliver their contents to the extracellular space. The molecular machinery involved is poorly understood. Here, we have used kinetic trafficking assays and transient CRISPR knock-outs to study the biosynthetic sorting route from the Golgi apparatus to the plasma membrane. Depletion of core-exocyst subunits reduces carrier fusion and causes cargo accumulation in the post-Golgi carriers. Exocyst subunits co-localise with carriers fusing at the plasma membrane and we show that the exocyst complex is recruited directly to these carriers. Abrogation of exocyst followed by kinetic trafficking assays with multiple different soluble cargoes results in cargo accumulation of all tested cargoes. Unbiased secretomics reveals a drastic reduction in the secretion of soluble proteins to the extracellular milieu after knock-out of exocyst subunits. Importantly, the knock-out of exocyst subunits in specialised secretory cell types prevents the constitutive secretion of antibodies in lymphocytes and of the hormones leptin and adiponectin in adipocytes. Together these data identify the exocyst complex as the functional tether of secretory post-Golgi carriers at the plasma membrane and an essential component of the mammalian constitutive secretory pathway.