bluuebunny/crossref_metadata_2025 huggingface dataset:
Murine norovirus virulence factor 1 (VF1) protein contributes to viral fitness during persistent infection
Authors: Borg Constantina , Jahun Aminu S. , Thorne Lucy , Sorgeloos Frédéric , Bailey Dalan , Goodfellow Ian G.
Published: September 2021

Murine norovirus (MNV) is widely used as a model for studying norovirus biology. While MNV isolates vary in their pathogenesis, infection of immunocompetent mice mostly results in persistent infection. The ability of a virus to establish a persistent infection is dependent on its ability to subvert or avoid the host immune response. Previously, we described the identification and characterization of virulence factor 1 (VF1) in MNV, and demonstrated its role as an innate immune antagonist. Here, we explore the role of VF1 during persistent MNV infection in an immunocompetent host. Using reverse genetics, we generated MNV-3 viruses carrying a single or a triple termination codon inserted in the VF1 ORF. VF1-deleted MNV-3 replicated to comparable levels to the wildtype virus in tissue culture. Comparative studies between MNV-3 and an acute MNV-1 strain show that MNV-3 VF1 exerts the same functions as MNV-1 VF1, but with reduced potency. C57BL/6 mice infected with VF1-deleted MNV-3 showed significantly reduced replication kinetics during the acute phase of the infection, but viral loads rapidly reached the levels seen in mice infected with wildtype virus after phenotypic restoration of VF1 expression. Infection with an MNV-3 mutant that had three termination codons inserted into VF1, in which reversion was suppressed, resulted in consistently lower replication throughout a 3 month persistent infection in mice, suggesting a role for VF1 in viral fitness in vivo. Our results indicate that VF1 expressed by a persistent strain of MNV also functions to antagonize the innate response to infection. We found that VF1 is not essential for viral persistence, but instead contributes to viral fitness in mice. These data fit with the hypothesis that noroviruses utilize multiple mechanisms to avoid and/or control the host response to infection and that VF1 is just one component of this.
Revisiting the heterogeneous global genomic population structure of Leishmania infantum
Authors: Patino Luz H. , Castillo-Castañeda Adriana , Muñoz Marina , Muskus Carlos , Rivero-Rodríguez Matilde , Pérez-Doria Alveiro , Bejarano Eduar E. , Ramírez Juan David
Published: September 2021

Leishmania infantum is the main causative agent responsible for visceral leishmaniasis (VL), a disease with global distribution. The genomic structure and genetic variation of this species have been widely studied in different parts of the world. However, in some countries, this information is still yet unknown, as is the genomic behaviour of the main antigens used in VL diagnosis (rK39 and rK28), which have demonstrated variable sensitivity and specificity in a manner dependent on the geographic region analysed. The objective of this study was to explore the genomic architecture and diversity of four Colombian L. infantum isolates obtained in this study and to compare these results with the genetic analysis of 183 L. infantum isolates from across the world (obtained from public databases), as well as to analyse the whole rK39 and rK28 antigen sequences in our dataset. The results showed that, at the global level, L. infantum has high genetic homogeneity and extensive aneuploidy. Furthermore, we demonstrated that there are distinct populations of L. infantum circulating in various countries throughout the globe and that populations of distant countries have close genomic relationships. Additionally, this study demonstrated the high genetic variability of the rK28 antigen worldwide. In conclusion, our study allowed us to (i) expand our knowledge of the genomic structure of global L. infantum; (ii) describe the intra-specific genomic variability of this species; and (iii) understand the genomic characteristics of the main antigens used in the diagnosis of VL. Additionally, this is the first study to report whole-genome sequences of Colombian L. infantum isolates.
Immune responses in COVID-19 respiratory tract and blood reveal mechanisms of disease severity
Authors: Zhang Wuji , Chua Brendon Y. , Selva Kevin J. , Kedzierski Lukasz , Ashhurst Thomas M. , Haycroft Ebene R. , Shoffner Suzanne K. , Hensen Luca , Boyd David F. , James Fiona , Mouhtouris Effie , Kwong Jason C. , Chua Kyra Y. L. , Drewett George , Copaescu Ana , Dobson Julie E. , Rowntree Louise C. , Habel Jennifer R. , Allen Lilith F. , Koay Hui-Fern , Neil Jessica A. , Gartner Matthew , Lee Christina Y. , Andersson Patiyan , Seemann Torsten , Sherry Norelle L. , Amanat Fatima , Krammer Florian , Londrigan Sarah L. , Wakim Linda M. , King Nicholas J.C. , Godfrey Dale I. , Mackay Laura K. , Thomas Paul G. , Nicholson Suellen , Arnold Kelly B. , Chung Amy W. , Holmes Natasha E. , Smibert Olivia C. , Trubiano Jason A. , Gordon Claire L. , Nguyen Thi H.O. , Kedzierska Katherine
Published: September 2021

Although the respiratory tract is the primary site of SARS-CoV-2 infection and the ensuing immunopathology, respiratory immune responses are understudied and urgently needed to understand mechanisms underlying COVID-19 disease pathogenesis. We collected paired longitudinal blood and respiratory tract samples (endotracheal aspirate, sputum or pleural fluid) from hospitalized COVID-19 patients and non-COVID-19 controls. Cellular, humoral and cytokine responses were analysed and correlated with clinical data. SARS-CoV-2-specific IgM, IgG and IgA antibodies were detected using ELISA and multiplex assay in both the respiratory tract and blood of COVID-19 patients, although a higher receptor binding domain (RBD)-specific IgM and IgG seroconversion level was found in respiratory specimens. SARS-CoV-2 neutralization activity in respiratory samples was detected only when high levels of RBD-specific antibodies were present. Strikingly, cytokine/chemokine levels and profiles greatly differed between respiratory samples and plasma, indicating that inflammation needs to be assessed in respiratory specimens for the accurate assessment of SARS-CoV-2 immunopathology. Diverse immune cell subsets were detected in respiratory samples, albeit dominated by neutrophils. Importantly, we also showed that dexamethasone and/or remdesivir treatment did not affect humoral responses in blood of COVID-19 patients. Overall, our study unveils stark differences in innate and adaptive immune responses between respiratory samples and blood and provides important insights into effect of drug therapy on immune responses in COVID-19 patients.
Prenatal Selective Serotonin Reuptake Inhibitor Exposure, Depression and Brain Morphology in Middle Childhood: Results from the ABCD Study
Authors: Moreau Allison L. , Voss Michaela , Hansen Isabella , Paul Sarah E. , Barch Deanna M. , Rogers Cynthia E. , Bogdan Ryan
Published: September 2021

Objective

Prenatal selective serotonin reuptake inhibitor (SSRI) exposure has been inconsistently linked to depression. Potential neural intermediaries remain understudied. We examined whether prenatal SSRI exposure is associated with depressive symptoms and brain structure during middle childhood.

Methods

Prenatal SSRI exposure (retrospective caregiver-report), depressive symptoms (caregiver-reported Child Behavior Checklist) and brain structure (MRI-derived subcortical volume; cortical thickness and surface area) were assessed in children (analytic ns=5,420-7,528; 235 with prenatal SSRI exposure; 9-10 years old) who completed the baseline session of the Adolescent Brain and Cognitive DevelopmentSM Study. Covariates included familial (e.g., 1st degree relative depression density), pregnancy (e.g., planned pregnancy), and child (e.g., birthweight) variables. Matrix spectral decomposition was used to address multiple testing.

Results

There was no evidence that prenatal SSRI exposure was associated with child depression after accounting for recent maternal depressive symptoms. Prenatal SSRI exposure was associated with greater left superior parietal surface area (b=145.3 mm2, p=0.00038) and lateral occipital cortical thickness (b=0.0272 mm, p=0.0000079), neither of which was associated with depressive symptoms.

Conclusions

Our findings, combined with adverse associations of prenatal exposure to maternal depression and the utility of SSRIs for treating depression, suggest that risk for child depression during middle childhood should not discourage SSRI use during pregnancy. It will be important for future work to examine associations between prenatal SSRI exposure and depression through young adulthood, when risk for depression increases.
Circulating Tumour DNA Analysis Informing Adjuvant Chemotherapy in Stage II Colon Cancer (DYNAMIC Trial): Statistical Analysis Plan
Authors: Tie Jeanne , Lo Serigne N. , Cohen Joshua D. , Wang Yuxuan , Wong Rachel , Shapiro Jeremy , Harris Sam , Khattak Adnan , Burge Matthew , Vogelstein Bert , Gibbs Peter
Published: September 2021

Background

Detection of circulating tumour DNA (ctDNA) after curative intent treatment reflects the presence of minimal residual disease and predicts for recurrence. DYNAMIC trial is a randomised phase II investigating the clinical utility of ctDNA-guided adjuvant treatment strategy compared with the standard of care (non-ctDNA based) approach in patients with stage II colon cancer. The primary trial endpoint is recurrence-free survival estimated from Kaplan Meier Method at 2 years. Secondary endpoints include proportion of patients treated with adjuvant chemotherapy, time-to-recurrence, overall survival, ctDNA clearance rate (investigational arm) and quality-adjusted life-years.

Objective

To outline and publish the pre-determined statistical analysis plan (SAP) before the database lock and the start of analysis.

Methods

The SAP describes basic analysis principles, methods for dealing with a range of commonly encountered data analysis issues and the specific statistical procedures for analysing efficacy and safety outcomes. The SAP was approved after closure of recruitment and before completion of patient follow-up. It outlines the planned primary analyses and a range of subgroup and sensitivity analyses regarding the clinical outcomes. Health economic outcomes are not included in this plan but will be analysed separately. The SAP will be adhered to for the final data analysis of this trial to avoid analysis bias arising from knowledge of the data.

Trial Registration

ANZ Clinical Trials Registry, ACTRN12615000381583. Registered on 27th April 2015.
Covid spirals: a phase diagram representation of COVID-19 effective reproduction number Rt
Authors: Pesenti K. W. , Pesenti R.
Published: September 2021

In this paper, we propose a phase diagram representation of COVID-19 effective reproduction number Rt. Specifically, we express Rt as a function of the estimated infected individuals. This function plots a particular clockwise spiral that allows to easily compare the evolution of the number of new infected individuals at different dates and, possibly, provide some hints on the future progression of the infection.
COVID-19 Vaccine Efficacy in a Diverse Urban Healthcare Worker Population
Authors: Iliaki Eirini , Lan Fan-Yun , Christophi Costas A. , Guidotti Guido , Jobrack Alexander D. , Buley Jane , Nathan Neetha , Osgood Rebecca , Bruno-Murtha Lou Ann , Kales Stefanos N.
Published: September 2021

Objective

To investigate COVID-19 vaccine efficacy (VE) among healthcare workers (HCWs) in an ethnically diverse community healthcare system, during its initial immunization campaign.

Methods

HCWs of the system were retrospectively included from the beginning of a COVID-19 vaccination program (December 16, 2020) until March 31, 2021. Those with a prior COVID-19 infection before December 15 were excluded. The Occupational Health department of the system ran a COVID-19 screening and testing referral program for workers, consistently throughout the study period. A master database had been established and updated comprising of the demographics, COVID-19 PCR assays, and vaccinations of each HCW. Andersen-Gill extension of the Cox models were built to estimate the VE of fully/partially vaccinated person-days at risk.

Results

Among the 4317 eligible HCWs, 3249 (75%) received any vaccination during the study period. Vaccinated HCWs were older, less likely to be Black/African American, Hispanic/Latino or identify as two or more races, and more likely to be medical providers. After adjusting for age, sex, race, and the statewide background incidence at the time of vaccination, we observed a VE of 80.2% (95% CI: 57.5–90.8%) for ≧14 days after the first dose of Pfizer/Moderna, and 95.5% (95% CI: 88.2-98.3%) among those fully vaccinated (i.e. ≧14 days after the second dose of Pfizer/Moderna or the single dose of J&J/Janssen).

Conclusion

COVID-19 vaccine effectiveness in the real world is promising, and these data in concert with culturally appropriate may decrease vaccine hesitancy.
A randomized controlled trial of antibody response to 2019-20 cell-based inactivated and egg-based live attenuated influenza vaccines in children and young adults
Authors: Williams Katherine V. , Zhai Bo , Alcorn John F. , Nowalk Mary Patricia , Levine Min Z. , Kim Sara S. , Flannery Brendan , Geffel Krissy Moehling , Merranko Amanda Jaber , Nagg Jennifer P. , Collins Mark , Susick Michael , Clarke Karen S. , Zimmerman Richard K. , Martin Judith M.
Published: September 2021

Background

Hemagglutination inhibition (HAI) titers to the live-attenuated influenza vaccine (LAIV4) are typically lower than its counterpart egg-based inactivated influenza vaccines (IIV). Similar comparisons have not been made between LAIV4 and the 4-strain, cell-culture inactivated influenza vaccine (ccIIV4). We compared healthy children and young adult HAI titers against the 2019-2020 LAIV4 and ccIIV4.

Methods

Participants aged 4-21 years were randomized 1:1 to receive ccIIV4 (n =100) or LAIV4 (n=98). Blood was drawn prevaccination and on day 28 (21-35) post vaccination. HAI assays against egg-grown A/H1N1, A/H3N2, both vaccine B strains and cell-grown A/H3N2 antigens were conducted. Outcomes were geometric mean titers (GMT) and geometric mean fold rise (GMFR) in titers.

Results

GMTs to A/H1N1, A/H3N2 and B/Victoria increased following both ccIIV and LAIV and to B/Yamagata following ccIIV (p<0.05). The GMFR range was 2.4-3.0 times higher for ccIIV4 than for LAIV4 (p<0.001). Within vaccine types, egg-grown A/H3N2 GMTs were higher (p<0.05) than cell-grown GMTs [ccIIV4 day 28: egg=205 (95% CI: 178-237); cell=136 (95% CI:113-165); LAIV4 day 28: egg=96 (95% CI: 83-112); cell=63 (95% CI: 58-74)]. The GMFR to A/H3N2 cell-grown and egg-grown antigens were similar. Pre-vaccination titers inversely predicted GMFR.

Conclusion

The HAI response to ccIIV4 was greater than LAIV4 in this study of mostly older children, and day 0 HAI titers inversely predicted GMFR for both vaccines. For both vaccines, the A/H3N2 cell-grown antigen levels were lower than egg-grown, but the GMFR for cell-grown and egg-grown did not differ significantly within vaccine type.

Clinical Trials No

NCT03982069
Association Between SARS-CoV-2 RNAemia and Post-Acute Sequelae of COVID-19
Authors: Ram-Mohan Nikhil , Kim David , Rogers Angela J , Blish Catherine A , Nadeau Kari C , Blomkalns Andra L , Yang Samuel
Published: September 2021

Determinants of Post-Acute Sequelae of COVID-19 are not known. Here we show that 75% of patients with viral RNA in blood (RNAemia) at presentation were symptomatic in the post-acute phase. RNAemia at presentation successfully predicted PASC, independent of patient demographics, initial disease severity, and length of symptoms.
Brain age as a surrogate marker for information processing speed in multiple sclerosis
Authors: Denissen S , Engemann DA , De Cock A , Costers L , Baijot J , Laton J , Penner IK , Grothe M , Kirsch M , D’hooghe MB , D’Haeseleer M , Dive D , De Mey J , Van Schependom J , Sima DM , Nagels G
Published: September 2021

Background

Data from neuro-imaging techniques allow us to estimate a brain’s age. Brain age is easily interpretable as “how old the brain looks”, and could therefore be an attractive communication tool for brain health in clinical practice. This study aimed to investigate its clinical utility.

Objectives

To investigate the relationship between brain age and information processing speed in MS.

Methods

A ridge-regression model was trained to predict age from brain MRI volumetric features and sex in a healthy control dataset (HC_train, n=1690). This model was used to predict brain age in two test sets: HC_test (n=50) and MS_test (n=201). Brain-Predicted Age Difference (BPAD) was calculated as BPAD=brain age minus chronological age. Information processing speed was assessed with the Symbol Digit Modalities Test (SDMT).

Results

Brain age was significantly related to SDMT scores in the MS_test dataset (r=-0.44, p<.001), and contributed uniquely to variance in SDMT beyond chronological age, reflected by a significant correlation between BPAD and SDMT (r=-0.21, p=0.003) and a significant weight (−0.21, p=0.011) in a multivariate regression equation with age.

Conclusions

Brain age is a candidate biomarker for information processing speed in MS and an easy to grasp metric for brain health.
UTTARAKHAND COVID-19 CASES AND DEATHS: COMPARING THE DEMOGRAPHICS AND SUGGESTIVE STRATEGY TO PREVENT SIMILAR PANDEMICS IN FUTURE
Authors: Joshi Gaurav , Pande Akshara , Gupta Omdeep , Nautiyal Anoop , Jasola Sanjay , Gahtori Prashant
Published: September 2021

Coronavirus disease 19 (Covid-19) is causing a dramatic impact on human life worldwide. As of June 11 2021, later one has attributed more than 174 million confirmed cases and over 3.5 million deaths globally. Nonetheless, a World Bank Group flagship report features Covid-19 induced global crisis as the strongest post-recession since World WarII. Currently, all approved therapeutics or vaccines are strictly allowed for emergency use. Hence, in the absence of pharmaceutical interventions, it is vital to analyze data set covering the growth rates of positive human cases, number of recoveries, other factors, and future strategies to manage the growth of fatal Covid-19 effectively. The Uttarakhand state of India is snuggled in the lap of the Himalayas and occupies more people than Israel, Switzerland, Hong Kong, etc. This study analyzed state Covid-19 data, fetched from an authenticated government repository using Python 3.9 from April 1, 2020, to February 28, 2021. In the first wave, plain areas of Uttarakhand covering the districts Dehradun, Haridwar, Nainital, and U. S. Nagar were severely affected and reported peak positive cases during the 21st – 26th week. Other hands, the hilly terrains of Uttarakhand districts, including Chamoli, Pauri Garhwal, and Rudraprayag, reported a high number of positive cases between the 30th and 31st week, and other hilly districts reported an increase in Covid-19 cases during the 34th to 38th week. The highest recovery rate was attributed to the hilly district Rudraprayag. The analysis also revealed that a very high doubling rate was seen during the last week of May to the first week of Jun 2020. At last, based on this blueprint, we have suggested 6-points solutions for preventing the next pandemic.
Unraveling the COVID-19 hospitalization dynamics in Spain using publicly available data
Authors: Aleta Alberto , Blas-Laína Juan Luis , Anglés Gabriel Tirado , Moreno Yamir
Published: September 2021

Background

One of the main challenges of the ongoing COVID-19 pandemic is to be able to make sense of available, but often heterogeneous and noisy data, to characterize the evolution of the SARS-CoV-2 infection dynamics, with the additional goal of having better preparedness and planning of healthcare services. This contribution presents a data-driven methodology that allows exploring the hospitalization dynamics of COVID-19, exemplified with a study of 17 autonomous regions in Spain.

Methods

We use data on new daily cases and hospitalizations reported by the Ministry of Health of Spain to implement a Bayesian inference method that allows making short and mid-term predictions of bed occupancy of COVID-19 patients in each of the autonomous regions of the country.

Findings

We show how to use given and generated temporal series for the number of daily admissions and discharges from hospital to reproduce the hospitalization dynamics of COVID-19 patients. For the case-study of the region of Aragon, we estimate that the probability of being admitted to hospital care upon infection is 0·090 [0·086-0·094], (95% C.I.), with the distribution governing hospital admission yielding a median interval of 3·5 days and an IQR of 7 days. Likewise, the distribution on the length of stay produces estimates of 12 days for the median and 10 days for the IQR. A comparison between model parameters for the regions analyzed allows to detect differences and changes in policies of the health authorities.

Interpretation

The amount of data that is currently available is limited, and sometimes unreliable, hindering our understanding of many aspects of this pandemic. We have observed important regional differences, signaling that to properly compare very different populations, it is paramount to acknowledge all the diversity in terms of culture, socio-economic status and resource availability. To better understand the impact of this pandemic, much more data, disaggregated and properly annotated, should be made available.
Impact and Equality of Expanding Pre-Exposure Prophylaxis (PrEP) for Men who have Sex with Men in Los Angeles County
Authors: Nguyen Anthony , Drabo Emmanuel Fulgence , Garland Wendy , Moucheraud Corrina , Holloway Ian W , Leibowitz Arleen , Suen Sze-chuan
Published: September 2021

Background

Racial and ethnic minority men who have sex with men (MSM) are disproportionately affected by HIV/AIDS in Los Angeles County (LAC), an important epicenter in the battle to end HIV.

Objective

To examine tradeoffs between effectiveness and equality of PrEP allocation strategies among different racial and ethnic groups of MSM in LAC.

Design, Setting, and Population

We developed a microsimulation model of HIV among MSM in LAC using county epidemic surveillance and survey data to capture demographic trends and subgroup-specific partnership patterns, disease progression, patterns of PrEP use, and patterns for viral suppression.

Intervention

We simulated interventions where an additional 3000, 6000, or 9000 PrEP prescriptions are provided annually in addition to current levels, following different allocation scenarios to each racial/ethnic group (Black, Hispanic, or White).

Measurements

We estimated cumulative infections averted and measures of equality, after 15 years (2021-2035), relative to base case (no intervention).

Results

Of the policies evaluated, targeting PrEP preferentially to Black individuals would result in the largest reductions in incidence and disparities. This outcome was robust to different partnership preference assumptions, though the magnitude of impact differs.

Limitations

We limit analysis to MSM, who bear the majority of HIV/AIDS burden in LAC. We do not consider transmission via injection drug use or mother-to-child transmission, nor do we capture individual network transmission effects. We assume no improvements in the prevention-diagnosis-treatment cascade besides increased PrEP use.

Conclusions

We find there is little trade-off between effectiveness and equality of outcome when choosing groups to target for PrEP in LAC – by focusing on MSM with the highest HIV incidence (Black), we can reduce both overall infections and racial/ethnic disparities.
Synaptic and intrinsic mechanisms impair reticular thalamus and thalamocortical neuron function in a Dravet syndrome mouse model
Authors: Studtmann Carleigh , Ladislav Marek , Topolski Mackenzie A. , Safari Mona , Swanger Sharon A.
Published: September 2021

Thalamocortical network dysfunction contributes to seizures and sleep deficits in Dravet syndrome (DS), an infantile epileptic encephalopathy, but the underlying molecular and cellular mechanisms remain elusive. DS is primarily caused by mutations in the SCN1A gene encoding the voltage-gated sodium channel NaV1.1, which is highly expressed in GABAergic reticular thalamus (nRT) neurons as well as glutamatergic thalamocortical neurons. We hypothesized that NaV1.1 haploinsufficiency alters somatosensory corticothalamic circuit function through both intrinsic and synaptic mechanisms in nRT and thalamocortical neurons. Using Scn1a heterozygous mice of both sexes aged P25-P30, we discovered reduced intrinsic excitability in nRT neurons and thalamocortical neurons in the ventral posterolateral (VPL) thalamus, while thalamocortical ventral posteromedial (VPM) neurons exhibited enhanced excitability. NaV1.1 haploinsufficiency enhanced GABAergic synaptic input and reduced ascending glutamatergic sensory input to VPL neurons, but not VPM neurons. In addition, glutamatergic cortical input to nRT neurons was reduced in Scn1a heterozygous mice, whereas cortical input to VPL and VPM neurons remained unchanged. These findings introduce input-specific alterations in glutamatergic synapse function and aberrant glutamatergic neuron excitability in the thalamus as disease mechanisms in Dravet syndrome, which has been widely considered a disease of GABAergic neurons. This work reveals additional complexity that expands current models of thalamic dysfunction in Dravet syndrome and identifies new components of corticothalamic circuitry as potential therapeutic targets.

HIGHLIGHTS

GABAergic reticular thalamus neurons have impaired tonic and burst firing properties in a NaV1.1 haploinsufficiency mouse model of Dravet syndrome.

NaV1.1 haploinsufficiency has opposing effects on spike firing in two distinct glutamatergic thalamocortical neuron populations.

NaV1.1 haploinsufficiency alters glutamatergic synaptic connectivity in an input-specific manner in the thalamus.

Dysregulation of both intrinsic and synaptic mechanisms contribute to imbalanced thalamic excitation and inhibition in this Dravet syndrome mouse model.
A subset of nucleus accumbens neurons receiving dense and functional prelimbic cortical input are required for cocaine seeking
Authors: Siemsen Benjamin M. , Barry Sarah M. , Vollmer Kelsey , Green Lisa M. , Brock Ashley G. , Westphal Annaka M. , King Raven A. , DeVries Derek M. , Otis James M. , Cowan Christopher W. , Scofield Michael D.
Published: September 2021

Background

Prelimbic cortical projections to the nucleus accumbens core are critical for cue-induced cocaine seeking, but the identity of the accumbens neuron(s) targeted by this projection, and the transient neuroadaptations contributing to relapse within these cells, remain unknown.

Methods

Male Sprague-Dawley rats underwent cocaine or sucrose self-administration, extinction, and cue-induced reinstatement. Pathway-specific chemogenetics, patch-clamp electrophysiology, in vivo electrochemistry, and high-resolution confocal microscopy were used to identify and characterize a small population of nucleus accumbens core neurons that receive dense prelimbic cortical input to determine their role in regulating cue-induced cocaine and natural reward seeking.

Results

Chemogenetic inhibition of prelimbic cortical projections to the nucleus accumbens core suppressed cue-induced cocaine relapse and normalized real-time cue-evoked increases in accumbens glutamate release to that of sucrose seeking animals. Furthermore, chemogenetic inhibition of the population of nucleus accumbens core neurons receiving the densest prelimbic cortical input suppressed cocaine, but not sucrose seeking. These neurons also underwent morphological plasticity during the peak of cocaine seeking in the form of dendritic spine expansion and increased ensheathment by astroglial processes at large spines.

Conclusions

We identified and characterized a unique subpopulation of nucleus accumbens neurons that receive dense prelimbic cortical input. The functional specificity of this subpopulation is underscored by their ability to mediate cue-induced cocaine relapse, but not sucrose seeking. This subset of cells represents a novel target for addiction therapeutics revealed by anterograde targeting to interrogate functional circuits imbedded within a known network.
Immunosuppression and Outcomes in Acute Myeloid Leukemia
Authors: Ferraro Francesca , Miller Christopher , Christensen Keegan , Helton Nichole M. , O'Laughlin Margareth , Fronick Catrina C , Fulton Robert S , Kohlschmidt Jessica , Eisfeld Ann-Kathrin , Bloomfield Clara D , Ramakrishnan Sai M , Day Ryan B , Wartman Lukas D , Uy Geoffrey L , Welch John S , Christopher Matthew J , Heath Sharon E , Baty Jack D , Schuelke Matthew J , Payton Jacqueline E , Spencer David H , Rettig Michael P , Link Daniel C , Walter Matthew J , Peter Westervelt , DiPersio John F , Ley Timothy J
Published: September 2021

Acute myeloid leukemia (AML) patients rarely have long first remissions (> 5 years) after standard-of-care chemotherapy, unless classified as favorable risk at presentation. Identification of the mechanisms responsible for long vs. more typical, short remissions may help to define prognostic determinants for chemotherapy responses. Using exome sequencing, RNA sequencing and functional immunologic studies, we characterized 28 Normal Karyotype (NK)-AML patients with >5 year first remissions after chemotherapy (Long First Remissions, LFR) and compared them to a well-matched group of 31 NK-AML patients who relapsed within 2 years (Standard First Remissions, SFR). Our combined analyses indicated that genetic risk profiling at presentation (as defined by ELN 2017 Criteria) was not sufficient to explain the outcomes of many SFR cases. Single cell RNA-sequencing studies of 15 AML samples showed that SFR AML cells differentially expressed many genes associated with immune suppression. The bone marrow of SFR cases had significantly fewer CD4+ Th1 cells; these T cells expressed an exhaustion signature and were resistant to activation by T-cell receptor stimulation in the presence of autologous AML cells. T cell activation could be restored by removing the AML cells, or blocking the inhibitory MHC Class II receptor, LAG3. Most LFR cases did not display these features, suggesting that their AML cells were not as immunosuppressive. These findings were confirmed and extended in an independent set of 50 AML cases representing all ELN 2017 risk groups. AML cell-mediated suppression of CD4+ Tcell activation at presentation is strongly associated with unfavorable outcomes in AML patients treated with standard chemotherapy.
Comments on a small sabretooth cat in the Abismo Ponta de Flecha Cave, Vale do Ribeira, southeastern Brazil
Authors: Chahud Artur
Published: September 2021

The Vale do Ribeira, located in southeastern Brazil, is known for many caves with osteological material, including several extinct species. The saber-tooth cat Smilodon populator was a large predator that inhabited the Pleistocene and Holocene of South America. A specimen found in the Abismo Ponta de Flecha Cave based on small bones (metacarpals and phalanges) is commented here. The metacarpals have morphological characteristics of S. populator, but are smaller than that of S. fatalis and Panthera onca and larger than that of S. gracilis. The specimen is among the smallest ever found and is comparable in size to an adult lion.
Electrical impulse characterization along actin filaments in pathological conditions
Authors: Hunley Christian , Mohsin Md , Marucho Marcelo
Published: September 2021

We present an interactive Mathematica notebook that characterizes the electrical impulses along actin filaments in both muscle and non-muscle cells for a wide range of physiological and pathological conditions. The program is based on a multi-scale (atomic → monomer → filament) approach capable of accounting for the atomistic details of a protein molecular structure, its biological environment, and their impact on the travel distance, velocity, and attenuation of monovalent ionic wave packets propagating along microfilaments. The interactive component allows investigators to conduct original research by choosing the experimental conditions (intracellular Vs in vitro), nucleotide state (ATP Vs ADP), actin isoform (alpha, gamma, beta, and muscle or non-muscle cell), as well as, a conformation model that covers a variety of mutants and wild-type (the control) actin filament. The simplicity of the theoretical formulation and the high performance of the Mathematica software enable the analysis of multiple conditions without computational restrictions. These studies may provide an unprecedented molecular understanding of why and how age, inheritance, and disease conditions induce dysfunctions in the biophysical mechanisms underlying the propagation of electrical signals along actin filaments.
Clues to reaction specificity in PLP-dependent fold type I aminotransferases of monosaccharide biosynthesis
Authors: Srivastava Jaya , Balaji Petety V.
Published: September 2021

Novel functions can emerge in an enzyme family while conserving catalytic mechanism, motif or fold. PLP-dependent enzymes have evolved into seven fold-types and catalyse diverse reactions using the same mechanism for the formation of external aldimine. Nucleotide sugar aminotransferases (which will be henceforth referred to as aminotransferases) belong to fold type I and mediate the biosynthesis of several monosaccharides. They use diverse substrates but are highly selective to the C3 or C4 carbon to which amine group is transferred. Profile HMMs were able to identify aminotransferases but could not capture reaction specificity. A search for discriminating features led to the discovery of sequence motifs that are located near the pyranose binding site suggesting their role in imparting reaction specificity. Using a position weight matrix for this motif, we were able to assign reaction specificity to a large number of aminotransferases. Inferences from this analysis set way for future experiments that can shed light on mechanisms of functional diversification in nucleotide sugar aminotransferases of fold type I.
Aphid transmission of a Potexvirus, Foxtail mosaic virus, in the presence of the Potyvirus helper component proteinase
Authors: Jiang Jun , Yu Eric , Casteel Clare L.
Published: September 2021

To establish successful infections, plant viruses compete with the host plants for limited resources and thus alter the physiological state of the plants. After successful infection, insect vectors are required for the transmission of some plant viruses to the next host plant. One of the largest groups of plant viruses, the potyvirus, can be transmitted by aphids. During transmission, the potyvirus protein helper component proteinase (HC-Pro) binds to the yet-to-be-defined aphid receptor on the stylet, as well as to the virus particles through the Asp-Ala-Gly (DAG) motif of the viral coat protein. Previously it was determined that a naturally occurring DAG motif in the non-aphid transmissible potexvirus, Potato aucuba mosaic potexvirus (PAMV), is functional when the HC-Pro is provided through co-infection with a potyvirus. Further, the DAG motif of PAMV can be successfully transferred to another non-aphid transmissible potexvirus, Potato virus X (PVX), to convey aphid transmission capabilities. We expand on this previous work by demonstrating, the DAG motif from two different potyviruses, Sugarcane mosaic virus and Turnip mosaic virus, as well as the DAG motif from the previous potexvirus PAMV, can be added to another non-aphid transmissible potexvirus, Foxtail mosaic virus (FoMV), to make it aphid transmissible. Transmission efficiency varied from less than 10% to over 80% depending on the DAG motif and host plant used in transmission, suggesting not all DAG motifs are equal for engineering aphid transmission. The underlying mechanisms mediating this variation still need to be explored.
Involvement of Brn3a-positive spinal dorsal horn neurons in the transmission of visceral pain in inflammatory bowel disease model mice
Authors: Nishida Kazuhiko , Matsumura Shinji , Kobayashi Takuya
Published: September 2021

The spinal dorsal horn (SDH) plays a crucial role in the transmission and processing of somatosensory information. Although spinal neural circuits that process several distinct types of somatic sensations have been studied extensively, those responsible for visceral pain transmission remain poorly understood. In the present study, we analyzed dextran sodium sulfate (DSS)-induced inflammatory bowel disease (IBD) mouse models to characterize the spinal dorsal horn neurons involved in visceral pain transmission. Immunostaining for c-fos, a marker of neuronal activity, demonstrated that numerous c-fos-positive cells were found bilaterally in the lumbosacral spinal dorsal horn, and their distribution was particularly abundant in the shallow dorsal horn. Characterization of these neurons by several molecular markers revealed that the percentage of the Pit1-Oct1-Unc86 domain (POU domain)-containing transcription factor Brn3a-positive neurons among the c-fos-positive neurons in the shallow dorsal horn was 30-40% in DSS-treated mice, which was significantly higher than that in the somatic pain model mice. We further demonstrated by neuronal tracing that, within the shallow dorsal horn, Brn3a-positive neurons were more highly represented in spino-solitary projection neurons than in spino-parabrachial projection neurons. These results raise the possibility that Brn3a-positive spinal dorsal horn neurons make a large contribution to visceral pain transmission, part of which is mediated through the spino-solitary pathway.
Reversible supramolecular assembly of the anti-microbial peptide plectasin into helical non-amyloid fibrils
Authors: Pohl Christin , Effantin Gregory , Kandiah Eaazhisai , Meier Sebastian , Zeng Guanghong , Streicher Werner , Peters Günther H.J. , Schoehn Guy , Mueller-Dieckmann Christoph , Noergaard Allan , Harris Pernille
Published: September 2021

Self-assembly and fibril formation play important roles in protein behavior. Amyloid fibrils formation is well-studied due to its role in neurodegenerative diseases and characterized by refolding of the protein into predominant β-sheet form. However, much less is known about the assembly of proteins into other types of supramolecular structures. Using cryo-electron microscopy at a resolution of 1.97 Å, we show that a triple-mutant of the anti-microbial peptide plectasin assembles reversibly into helical non-amyloid fibrils. Plectasin contains a cysteine-stabilized α-helix-β-sheets structure, which remains intact upon fibril formation. Two fibrils form a right-handed superstructure with each fibril consisting of double helical, left-handed structures. The fibril formation is reversible and follows sigmoidal kinetics with a pH-dependent equilibrium between soluble monomer and protein fibril. The anti-microbial activity does not appear compromised by fibril formation. This is the first high-resolution structure of this type of α/β protein fibrils.
Ecology dictates the value of memory for foraging bees
Authors: Pull Christopher D. , Petkova Irina , Watrobska Cecylia , Pasquier Grégoire , Fernandez Marta Perez , Leadbeater Ellouise
Published: September 2021

“Ecological intelligence” hypotheses posit that animal learning and memory evolves to meet the demands posed by foraging, and together with social intelligence and cognitive buffer hypotheses, provide a key framework for understanding cognitive evolution. However, identifying the critical environments where cognitive investment reaps significant benefits has proved challenging. Here, we capitalise upon seasonal variation in forage availability for a social insect model (Bombus terrestris) to establish how the benefits of short-term memory vary with resource availability. Through analysis of over 1700 foraging trips carried out over two years, we show that short-term memory predicts foraging efficiency – a key determinant of colony fitness – in plentiful spring foraging conditions, but that this relationship is reversed during the summer floral dearth. Our results suggest that selection for enhanced cognitive abilities is unlikely to be limited to harsh environments where food is hard to find or extract, highlighting instead that the complexity of rich and plentiful environments could be a broad driver in the evolution of certain cognitive traits.
Actions of camptothecin derivatives on larvae and adults of the arboviral vectorAedes aegypti
Authors: Partridge Frederick A. , Poulton Beth C. , Lake Milly A.I. , Lees Rebecca A. , Mann Harry-Jack , Lycett Gareth J. , Sattelle David B
Published: September 2021

Mosquito-borne viruses including dengue, Zika and Chikungunya viruses as well as parasites such as malaria andOnchocerca volvulusendanger health and economic security around the globe and emerging mosquito-borne pathogens have pandemic potential. However, the rapid spread of insecticide resistance threatens our ability to control mosquito vectors. Larvae ofAedes aegypti(New Orleans strain) were screened with the Medicines for Malaria Venture Pandemic Response Box, an open-source compound library, using INVAPP, an invertebrate automated phenotyping platform suited to high-throughput chemical screening of larval motility.

Of the 400 compounds screened, we identified rubitecan (a synthetic derivative of camptothecin) as a hit compound that significantly reducedAe. aegyptilarval motility compared to DMSO controls. Both rubitecan and camptothecin displayed concentration dependent reduction in larval motility with estimated EC50s of 25.5 ± 5.0 μM and 22.3 ± 5.4 μM respectively. We extended our investigation to adult mosquitoes and found that camptothecin increased lethality when delivered in a blood meal toAe. aegyptiadults at 100 μM and 10 μM and completely blocked egg laying when fed at 100 μM.

Camptothecin and its derivatives, inhibitors of topoisomerase I, have known activity against several agricultural pests and are also approved for the treatment of several cancers. Crucially, they can inhibit Zika virus replication in human cells, so there is potential for dual targeting of both the vector and an important arbovirus that it carries. Both humans and mosquitoes express the highly conserved topoisomerase I target, however, the design of derivatives with differing pharmacokinetic properties may offer a promising route towards the development of insect-specificity of this chemistry.
Biochemical characterization of a human septin octamer
Authors: Fischer Martin , Frank Dominik , Rösler Reinhild , Johnsson Nils , Gronemeyer Thomas
Published: September 2021

1

Septins are part of the cytoskeleton and polymerize into non-polar filaments of heteromeric hexamers or octamers. They belong to the class of P-loop GTPases but the roles of GTP binding and hydrolysis on filament formation and dynamics are not well understood.

The basic human septin building block is the septin rod, a hetero-octamer composed of SEPT2, SEPT6, SEPT7, and SEPT9 with a stoichiometry of 2:2:2:2 (2-7-6-9-9-6-7-2).

Septin rods polymerize by end-to-end and lateral joining into linear filaments and higher ordered structures such as rings, sheets, and gauzes.

We purified a recombinant human septin octamer from E. coli for in vitro experimentation that is able to polymerize into filaments. We could show that the C-terminal region of the central SEPT9 subunit contributes to filament formation and that the human septin rod decreases the rate of in vitro actin polymerization.

We provide further first kinetic data on the nucleotide uptake- and exchange properties of human hexameric and octameric septin rods. We could show that nucleotide uptake prior to hydrolysis is a dynamic process and that a bound nucleotide is exchangeable. However, the hydrolyzed γ-phosphate is not released from the native protein complex. We consequently propose that GTP hydrolysis in human septins does not follow the typical mechanism known from other small GTPases.
Short-term instantaneous prophylaxis and efficient treatment against SARS-CoV-2 in hACE2 mice conferred by an intranasal nanobody (Nb22)
Authors: Wu Xilin , Wang Yaxing , Cheng Lin , Ni Fengfeng , Zhu Linjing , Ma Sen , Huang Bilian , Ji Mengmeng , Hu Huimin , Li Yuncheng , Xu Shijie , Shi Haixia , Zhang Doudou , Liu Linshuo , Nawaz Waqas , Hu Qinxue , Ye Sheng , Liu Yalan , Wu Zhiwei
Published: September 2021

Current COVID-19 vaccines need to take at least one month to complete inoculation and then become effective. Around 51% global population are still not fully vaccinated. Instantaneous protection is an unmet need among those who are not fully vaccinated. In addition, breakthrough infections caused by SARS-CoV-2 are widely reported. All these highlight the unmet needing for short-term instantaneous prophylaxis (STIP) in the communities where SARS-CoV-2 is circulating. Previously, we reported nanobodies isolated from an alpaca immunized with the spike protein, exhibiting ultrahigh potency against SARS-CoV-2 and its variants. Herein, we found that Nb22, among our previously reported nanobodies, exhibited ultrapotent neutralization against Delta variant with an IC50 value of 0.41 ng/ml (5.13 pM). Furthermore, the crystal structural analysis revealed that the binding of Nb22 to WH01 and Delta RBDs both effectively blocked the binding of RBD to hACE2. Additionally, intranasal Nb22 exhibited protection against SARS-CoV-2 Delta variant in the post-exposure prophylaxis (PEP) and pre-exposure prophylaxis (PrEP). Of note, intranasal Nb22 also demonstrated high efficacy against SARS-CoV-2 Delta variant in STIP for seven days administered by single dose and exhibited long-lasting retention in the respiratory system for at least one month administered by four doses, providing a means of instantaneous short-term prophylaxis against SARS-CoV-2. Thus, ultrahigh potency, long-lasting retention in the respiratory system as well as stability at room-temperature make the intranasal or inhaled Nb22 to be a potential therapeutic or STIP agent against SARS-CoV-2.

Brief summary

Nb22 exhibits ultrahigh potency against Delta variant in vitro and is exploited by crystal structural analysis; furthermore, animal study demonstrates high effectiveness in the treatment and short-term instantaneous prophylaxis in hACE2 mice via intranasal administration.

Highlights

Nb22 exhibits ultrapotent neutralization against Delta variant with an IC50 value of 0.41 ng/ml (5.13 pM).

Structural analysis elucidates the ultrapotent neutralization of Nb22 against Delta variant.

Nb22 demonstrates complete protection in the treatment of Delta variant infection in hACE2 transgenic mice.

We complete the proof of concept of STIP against SARS-CoV-2 using intranasal Nb22 with ultrahigh potency and long-lasting retention in respiratory system.

Graphic Abstract
Prider – multiplexed primer design using linearly scaling approximation of set coverage
Authors: Smolander Niina , Tamminen Manu
Published: September 2021

Designing oligonucleotide primers and probes is one of the key steps of various laboratory experiments such as multiplexed PCR or digital multiplexed ligation assays. When designing primers and probes to complex, heterogeneous DNA data sets, an optimization problem arises where the smallest number of oligonucleotides covering the largest diversity of the input dataset needs to be identified. Tools that provide this optimization in an efficient manner for large input data are currently lacking.

Here we present Prider, an R package for designing primers and probes with a nearly optimal coverage for complex and large sequence sets. Prider initially prepares a full primer coverage of the input sequences, the complexity of which is subsequently reduced by removing components of high redundancy or narrow coverage. The primers from the resulting near-optimal coverage are easily accessible as data frames and their coverage across the input sequences can be visualized as heatmaps using Prider’s plotting function. Prider scales linearly to increasing sequence data and therefore permits efficient design of primers to large and highly diverse DNA datasets.

Prider is available on GitHub under the permissive BSD-3-clause license:

https://github.com/manutamminen/prider