bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic dietary adaptation in Neandertal, Denisovan and Sapiens revealed by gene copy number variation
Authors: Vicedomini Riccardo , Righetti Niccolò , Polit Lélia , Condemi Silvana , Longo Laura , Carbone Alessandra
Published: November 2021

Dietary adaptation involves evolving an efficient system to digest food available in an ecosystem. The diet of archaic humans is traditionally reconstructed by isotopic analyses of human remains combined with the faunal assemblages found on the sites, and, recently, from metagenomic analyses of dental calculus. Here, we propose a new computational approach to find the genetic basis for human dietary adaptation. We searched 15 genomes from Neandertal, Denisovan and Early Sapiens for food digestion genes that tend to have more or fewer copies than the modern human reference genome. We identify 50 genes, including 10 gene clusters, with discernible copy number variation (CNV) trends at the population level, from an analysis of the full set of 20,000 human genes. The genomic variation of 19 of these genes shows how metabolic pathways for carbohydrates, lipids, liver lipids and brown fat in archaic humans adapted to metabolize food from animal or plant sources. The remaining 31 genes are all highly expressed in tissues of the digestive apparatus and are involved in immune response, environmental response and obesity. Analysis of the CNV profiles, compared to 64 modern human individuals belonging to distinct ethnic groups in Eurasia, Africa, Oceania, suggests thatHomo sapiensmay have had an evolutionary advantage compared to Neandertal and Denisovan in adapting to cold and temperate ecosystems.

Significance Statement

Understanding dietary strategies and foraging behaviors of past populations are among the goals of paleoanthropological and prehistoric studies. Based on a new computational approach, we seek for the genetic basis for human dietary adaptation. Gene copy number variation (CNV) is a major type of structural genome variation that we used as indicator of efficient metabolic processes for food digestion. By analysing billions of short sequences from 15 archaic human genomes and 64 modern human ones, across the full set of 20,000 human genes, we identify 50 genes whose population-wide discernable CNV trends point to lipid metabolism as being crucial for Neandertal, the efficiency in carbohydrate metabolism for Sapiens’ diet, and the importance of lipid metabolism and brown fat metabolism for both Neandertal and early Sapiens compared to modern humans.

Preprint availability:an early version, where the CNV analysis of ancient genomes was conducted on the human reference genome hg19, was deposited on BioRxiv on November 2, 2021 (DOI:10.1101/2021.10.30.466563). The current version, which utilises CNV estimates based on the human reference genome hg38 and includes comparisons with modern human populations, was deposited in BioRxiv in November 2024.
Proteomics reveals unique identities of human TGF-β-induced and thymus-derived CD4+ regulatory T cells
Authors: Mensink Mark , Schrama Ellen , Cuadrado Eloy , van den Biggelaar Maartje , Amsen Derk , de Kivit Sander , Borst Jannie
Published: November 2021

The CD4+ regulatory T (Treg) cell lineage, as defined by FOXP3 expression, comprises thymus-derived (t)Treg cells and peripherally induced (p)Treg cells. In human, naïve tTreg cells can be isolated from blood, while effector tTreg and pTreg cells cannot be purified reliably for lack of cell surface markers. As a model for Treg cells, studies often employ TGF-β-induced (i)Treg cells generated from CD4+ conventional T (Tconv) cells in vitro. Here, we describe the relationship of iTreg cells to tTreg and Tconv cells, as optimally purified from human blood. Proteomic analysis revealed that each of these cell populations has a unique protein expression pattern before and after CD3/CD28-mediated activation. iTreg cells had limited overlap in protein expression with tTreg cells and exhibited markedly differential expression of proteins involved in signal transduction and metabolism. Whereas iTreg and Tconv cells responded strongly to CD3/CD28-mediated activation, tTreg cells showed a modest response, which reflects their adaptations in signal transduction pathways. As a benchmark, we used a previously defined proteomic signature that discerns ex vivo naïve and effector Treg cells from Tconv cells and includes conserved Treg cell properties. This Treg cell core signature was largely absent in iTreg cells, as exemplified by STAT4 expression that may contribute to pro-inflammatory functions. In addition, we used a proteomic signature that distinguishes ex vivo effector Treg cells from Tconv cells and naïve Treg cells. This effector Treg cell signature was partially present in iTreg cells, indicating that they do have protein expression features in common with ex vivo effector Treg cells. In conclusion, iTreg cells are distinct from tTreg cells and largely lack the Treg cell core proteomic signature, indicating that caution is warranted when using iTreg cells as a model for Treg cell populations found in vivo.
Visceral Fat Inflammation and Fat Embolism are associated with Lung’s Lipidic Hyaline Membranes in COVID-19 patients
Authors: Colleluori Georgia , Graciotti Laura , Pesaresi Mauro , Di Vincenzo Angelica , Perugini Jessica , Di Mercurio Eleonora , Caucci Sara , Bagnarelli Patrizia , Zingaretti Cristina M. , Nisoli Enzo , Menzo Stefano , Tagliabracci Adriano , Ladoux Annie , Dani Christian , Giordano Antonio , Cinti Saverio
Published: November 2021

Background

Visceral obesity is a critical determinant of severe coronavirus disease-2019 (COVID-19). Methods: In this study, we performed a comprehensive histomorphologic analysis of autoptic visceral adipose tissues (VAT), lungs and livers of 19 COVID-19 and 23 non-COVID-19 subjects.

Results

Although there were no between-groups differences in body-mass-index and adipocytes size, higher prevalence of CD68+ macrophages in COVID-19 subjects’ VAT was detected (p=0.005) and accompanied by crown-like structures presence, signs of adipocytes stress and death. Consistently, human adipocytes were successfully infected by SARS-CoV2 in vitro and displayed lower cell viability. Being VAT inflammation associated with lipids spill-over from dead adipocytes, we studied lipids distribution employing Oil-Red-O staining (ORO). Lipids were observed within lungs and livers interstitial spaces, macrophages, endothelial cells, and vessels’ lumen, features suggestive of fat embolism syndrome, more prevalent among COVID-19 individuals (p<0.001). Notably, signs of fat embolism were more prevalent among obese (p=0.03) independently of COVID-19 diagnosis, suggesting that such condition may be an obesity complication, exacerbated by SARS-CoV2 infection. Importantly, all infected subjects’ lungs presented lipids-rich (ORO+) hyaline membranes, formations associated with COVID-19-related pneumonia, present only in one control with non-COVID-19 pneumonia.

Conclusions

This study describes for the first time novel COVID-19-related features possibly underlying the unfavorable prognosis in obese SARS-CoV2-infected-subjects.
Manual curation and phylogenetic analysis of chitinase family genes in the Asian citrus psyllid, Diaphorina citri
Authors: Shippy Teresa D. , Miller Sherry , Tamayo Blessy , Hosmani Prashant S , Flores-Gonzalez Mirella , Mueller Lukas A , Hunter Wayne B , Brown Susan J , D’Elia Tom , Saha Surya
Published: November 2021

Chitinases are enzymes that digest the polysaccharide polymer chitin. Chitin is a major component of insect exoskeletons, which must be replaced multiple times during growth and development in a process known as molting. Insect genomes usually have multiple chitinase genes, some of which are required for molting and some whose functions are still unknown. Since knockdown of the chitinases required for molting causes high levels of lethality, chitinase genes have drawn interest as targets for RNAi-based pest control methods. The Asian citrus psyllid, Diaphorina citri, carries the bacterium that causes Huanglongbing, also known as citrus greening disease, which is devastating the citrus industry worldwide. We have identified and annotated 12 chitinase family genes from D. citri as part of a community effort to create high quality gene models to facilitate the design of interdictory molecules for pest control. Using predicted protein domain content and phylogenetic analysis, we categorized the D. citri chitinases according to a previously established classification scheme and re-evaluated the classification of chitinases in other hemipterans. In addition to chitinases belonging to known groups, we identified a novel class of chitinases present in D. citri and several related hemipterans that appears to be the result of horizontal gene transfer.
Antibiotic inhibition of the Plasmodium apicoplast decreases haemoglobin degradation and antagonises dihydroartemisinin action
Authors: Crisafulli Emily M. , De Paoli Amanda , Tutor Madel V. , Siddiqui Ghizal , Creek Darren J. , Tilley Leann , Ralph Stuart A.
Published: November 2021

The World Health Organisation (WHO) recommends artemisinin (ART) combinations for treatment of uncomplicated Plasmodium falciparum malaria. Understanding the interaction between co-administered drugs within combination therapies is clinically important to prevent unintended consequences. The WHO guidelines recommend second line treatments that combine artesunate with tetracycline, doxycycline, or clindamycin—antibiotics that target the Plasmodium relict plastid, the apicoplast. In addition, antibiotics can be used simultaneously against other infectious diseases, leading to their inadvertent combination with ARTs. One consequence of apicoplast inhibition is a perturbation to haemoglobin uptake and trafficking—a pathway required for activation of ART derivatives. Here, we show that apicoplast-targeting antibiotics reduce the abundance of the catalyst of ART activation (free haem) in P. falciparum, likely through diminished haemoglobin digestion. We demonstrate antagonism between ART and these antibiotics, suggesting that apicoplast inhibitors reduce ART activation. These data have potential clinical implications due to the reliance on—and widespread use of—both ARTs and these antibiotics in malaria endemic regions.
Protective and aggressive bacterial subsets and metabolites modify hepatobiliary inflammation and fibrosis in PSC
Authors: Awoniyi Muyiwa , Wang Jeremy , Ngo Billy , Meadows Vik , Tam Jason , Viswanathan Amba , Lai Yunjia , Montgomery Stephanie A. , Farmer Morgan , Kummen Martin , Thingholm Louise B. , Schramm Christoph , Bang Corinna , Franke Andre , Schnabl Bernd , Lu Kun , Ting Jenny PY , Popov Yuri V. , Hov Johannes R. , Francis Heather , Sartor R. Balfour
Published: November 2021

Objective

Conflicting microbiota data exist for primary sclerosing cholangitis (PSC) and experimental models. Goal: Define complex interactions between resident microbes and their association in PSC patients by studying antibiotic-treated specific pathogen-free (SPF) and germ-free (GF) multi-drug-resistant 2 deficient (mdr2-/-) mice.

Design

We measured weights, liver enzymes, RNA expression, histological, immunohistochemical and fibrotic biochemical parameters, fecal 16s rRNA gene profiling, and metabolomic endpoints in gnotobiotic and antibiotic-treated SPF mdr2-/- mice and targeted metagenomic analysis in PSC patients.

Results

GF mdr2-/- mice had exaggerated hepatic inflammation and fibrosis with 100% mortality by 8 weeks; early SPF autologous stool transplantation rescued liver-related mortality. Broad-spectrum antibiotics and vancomycin alone accelerated disease in weanling SPF mdr2-/- mice, indicating that vancomycin-sensitive resident microbiota protect against hepatobiliary disease. Vancomycin treatment selectively decreased Lachnospiraceae and short-chain fatty acids (SCFAs) but expanded Enterococcus and Enterobacteriaceae. Antibiotics increased cytolysin-expressing E. faecalis and E. coli liver translocation; colonization of gnotobiotic mdr2-/- mice with translocated E. faecalis and E. coli strains accelerated liver inflammation and mortality. Lachnospiraceae colonization of antibiotic pre-treated mdr2-/- mice reduced liver fibrosis, inflammation and translocation of pathobionts, while Lachnospiraceae-produced SCFA decreased fibrosis. Fecal E. faecalis/ Enterobacteriaceae was positively and Lachnospiraceae was negatively associated with PSC patients’ clinical severity Mayo risk scores.

Conclusions

We identified specific functionally protective and detrimental resident bacterial species in mdr2-/- mice and PSC patients with associated clinical outcomes. These insights may guide personalized targeted therapeutic interventions in PSC patients.
The structure and organization of headache differential diagnoses: A Pilot Study of Subset Relationships between Differentials in ICHD3
Authors: Zhang Pengfei
Published: November 2021

Structured Abstract

Objective

Differential diagnosis is fundamental to medicine. Using DiffNet, a differential diagnosis generator, as a model we studied the structure and organization of how collections of diagnose (i.e. sets of diagnoses) are related in the ICHD3. Specifically, we asked: Which sets of differential diagnoses are subsets of each other? What is the minimum number of sets of differential diagnoses that encompass all ICHD3 codes? Furthermore, we explored the clinical and theoretical implication of these answers.

Methods

DiffNet is a freely distributed differential diagnosis generator for headaches using graph theoretical properties of ICHD3. For each ICHD3 diagnosis, we generated a set of differential diagnoses using DiffNet. We then determined algorithmically the set/subset relationship between these sets. We also determined the smallest list of ICHD3 diagnosis whose differential diagnoses would encompass the totality of ICHD3 diagnoses.

Results

All ICHD3 diagnoses can be represented by a minimum of 92 differential diagnosis sets. Differential diagnosis sets for 10 of the 14 first digit subcategories of ICHD3 are represented by more than one differential diagnosis sets. Fifty-one of the 93 differential diagnosis sets contain multiple subset relationships; the remaining 42 do not enter into any set/subset relationship with other differential diagnosis sets. Finally, we included a hierarchical presentation of differential diagnosis sets in ICHD3 according to DiffNet.

Conclusion

We propose a way of interpreting headache differential diagnoses as partial ordered sets (i.e. poset). For clinicians, fluency with the 93 diagnoses and their differential put forth here implies a complete description of ICHD3. On a theoretical level, interpreting ICHD3 differential diagnosis as poset, allows researchers to translate differential diagnoses sets topologically, algebraically, and categorically.
Report 46: Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals
Authors: Brizzi Andrea , Whittaker Charles , Servo Luciana M. S. , Hawryluk Iwona , Prete Carlos A. , de Souza William M. , Aguiar Renato S. , Araujo Leonardo J. T. , Bastos Leonardo S. , Blenkinsop Alexandra , Buss Lewis F. , Candido Darlan , Castro Marcia C. , Costa Silvia F. , Croda Julio , de Souza Santos Andreza Aruska , Dye Christopher , Flaxman Seth , Fonseca Paula L. C. , Geddes Victor E. V. , Gutierrez Bernardo , Lemey Philippe , Levin Anna S. , Mellan Thomas , Bonfim Diego M. , Miscouridou Xenia , Mishra Swapnil , Monod Mélodie , Moreira Filipe R. R. , Nelson Bruce , Pereira Rafael H. M. , Ranzani Otavio , Schnekenberg Ricardo P. , Semenova Elizaveta , Sonnabend Raphael , Souza Renan P. , Xi Xiaoyue , Sabino Ester C. , Faria Nuno R. , Bhatt Samir , Ratmann Oliver
Published: November 2021

The SARS-CoV-2 Gamma variant spread rapidly across Brazil, causing substantial infection and death waves. We use individual-level patient records following hospitalisation with suspected or confirmed COVID-19 to document the extensive shocks in hospital fatality rates that followed Gamma’s spread across 14 state capitals, and in which more than half of hospitalised patients died over sustained time periods. We show that extensive fluctuations in COVID-19 in-hospital fatality rates also existed prior to Gamma’s detection, and were largely transient after Gamma’s detection, subsiding with hospital demand. Using a Bayesian fatality rate model, we find that the geographic and temporal fluctuations in Brazil’s COVID-19 in-hospital fatality rates are primarily associated with geographic inequities and shortages in healthcare capacity. We project that approximately half of Brazil’s COVID-19 deaths in hospitals could have been avoided without pre-pandemic geographic inequities and without pandemic healthcare pressure. Our results suggest that investments in healthcare resources, healthcare optimization, and pandemic preparedness are critical to minimize population wide mortality and morbidity caused by highly transmissible and deadly pathogens such as SARS-CoV-2, especially in low- and middle-income countries.

Note

The following manuscript has appeared as ‘Report 46 - Factors driving extensive spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals’ at https://spiral.imperial.ac.uk:8443/handle/10044/1/91875.

One sentence summary

COVID-19 in-hospital fatality rates fluctuate dramatically in Brazil, and these fluctuations are primarily associated with geographic inequities and shortages in healthcare capacity.
Anti-SARS-CoV-2 vaccination does not induce the formation of autoantibodies but provides humoral immunity following heterologous and homologous vaccination regimens: Results from a clinical and prospective study within professionals of a German University Hospital
Authors: Thurm Christoph , Reinhold Annegret , Borucki Katrin , Kahlfuss Sascha , Feist Eugen , Schreiber Jens , Reinhold Dirk , Schraven Burkhart
Published: November 2021

By the end of 2019 a global pandemic by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV2) causing the coronavirus disease-19 (COVID-19) has emerged. Yet, COVID-19 represents a significant economic burden to healthcare systems, destabilizes global financial markets and has caused the death of almost 5 million people worldwide. In order to prevent severe disease courses of COVID-19 especially in elderly and to establish collective immunity on the long run, different vaccines have been developed, tested and were approved within a very short time period. In Germany, the first vaccines that have been approved by local authorities were AstraZeneca’s vector virus-based vaccine Vaxzevria and the mRNA vaccines Comirnaty and Spikevax, developed by BioNTech and Moderna, respectively. As it was reported that the novel coronavirus SARS-CoV2 can trigger autoimmunity, it is of significant interest to investigate whether anti-SARS-CoV2 vaccines evoke the formation of autoantibodies and subsequent autoimmunity. Here, we did set out to systematically analyze immune responses after homologous vaccinations with mRNA or vector virus-based vaccines or after heterologous Vector/mRNA vaccinations with respect to anti-COVID-19 immune responses and, in parallel, the development of autoantibodies. In our study, we obtained serum samples one day before and 14 as well as 28 days following booster vaccination and tested them for anti-SARS-CoV2 antibodies and for autoantibodies against Cardiolipin, Prothrombin, β2-Glycoprotein, cyclic citrullinated peptides (CCP), tissue-transglutaminase (TTG) and anti-nuclear antibodies (ANA). We find that compared to homologous mRNA and heterologous Vector/mRNA vaccination, anti-SARS-CoV2 antibody levels were 90% lower after homologous vector vaccination. Of note, heterologous Vector/mRNA vaccination was found to be more effective than homologous mRNA vaccination in terms of IgM and IgA responses against SARS-CoV2. However, in terms of autoantibody generation, we only detected increases after booster vaccination in participants with already pre-existing autoantibodies. In contrast, vaccinees showing no autoantibody formation before vaccination, did not respond with sustained autoantibody production upon vaccination. Taken together, our study suggests that all used SARS-CoV2 vaccines do not significantly foster autoantibody production over time but provide humoral immunity to SARS-CoV2.
Liquid-biopsy transcriptomic profiling uncovers molecular mediators of resistance to androgen receptor signaling inhibition in lethal prostate cancer
Authors: Zhang Jiaren , Zimmermann Bob , Galletti Giuseppe , Halabi Susan , Gjyrezi Ada , Yang Qian , Gupta Santosh , Verma Akanksha , Sboner Andrea , Anand Monika , George Daniel J. , Gregory Simon G. , Hong Seunghee , Pascual Virginia , Mavragani Clio P. , Antonarakis Emmanuel S. , Nanus David M. , Tagawa Scott T. , Elemento Olivier , Armstrong Andrew J. , Giannakakou Paraskevi
Published: November 2021

Androgen receptor signaling inhibitors (ARSi) are a mainstay for patients with metastatic castration-resistant prostate cancer (mCRPC). However, patient response is heterogeneous and the molecular underpinnings of ARSi resistance are not well elucidated. Here we performed transcriptome analysis of circulating tumor cells (CTCs) and peripheral blood mononuclear cells (PBMC) in the context of a prospective clinical trial of men with mCRPC treated with abiraterone (Abi) or enzalutamide (Enza). CTC RNA-sequencing identified that RB loss and enhanced E2F signaling along with BRCA loss transcriptional networks were associated with intrinsic ARSi resistance, while an inflammatory response signature was significantly associated with acquired resistance. Transcriptomic analysis of matching PBMCs identified enrichment of inflammasome gene signatures indicative of activated innate immunity at progression, with concurrent downregulation of T and NK cells. Importantly, CTC gene signatures had a significant positive association with circulating immune macroenvironment (CIME) signatures. Taken together, these data demonstrate that liquid biopsy transcriptomics can identify molecular pathways associated with clinical ARSi resistance paving the way for treatment optimization in patients with mCRPC.
Heart-brain connections: phenotypic and genetic insights from 40,000 cardiac and brain magnetic resonance images
Authors: Zhao Bingxin , Li Tengfei , Fan Zirui , Yang Yue , Wang Xifeng , Luo Tianyou , Tang Jiarui , Xiong Di , Wu Zhenyi , Chen Jie , Shan Yue , Tomlinson Chalmer , Zhu Ziliang , Li Yun , Stein Jason L. , Zhu Hongtu
Published: November 2021

Cardiovascular health interacts with cognitive and psychological health in complex ways. Yet, little is known about the phenotypic and genetic links of heart-brain systems. Using cardiac and brain magnetic resonance imaging (CMR and brain MRI) data from over 40,000 UK Biobank subjects, we developed detailed analyses of the structural and functional connections between the heart and the brain. CMR measures of the cardiovascular system were strongly correlated with brain basic morphometry, structural connectivity, and functional connectivity after controlling for body size and body mass index. The effects of cardiovascular risk factors on the brain were partially mediated by cardiac structures and functions. Using 82 CMR traits, genome-wide association study identified 80 CMR-associated genomic loci (P < 6.09 × 10-10), which were colocalized with a wide spectrum of heart and brain diseases. Genetic correlations were observed between CMR traits and brain-related complex traits and disorders, including schizophrenia, bipolar disorder, anorexia nervosa, stroke, cognitive function, and neuroticism. Our results reveal a strong heart-brain connection and the shared genetic influences at play, advancing a multi-organ perspective on human health and clinical outcomes.
Allelic Complexity of KMT2A Partial Tandem Duplications in Acute Myeloid Leukemia and Myelodysplastic Syndromes
Authors: Tsai Harrison K. , Gibson Christopher J. , Murdock H. Moses , Davineni Phani , Harris Marian H. , Wang Eunice S. , Gondek Lukasz P. , Kim Annette S. , Nardi Valentina , Lindsley R. Coleman
Published: November 2021

KMT2A partial tandem duplication (KMT2A-PTD) at 11q23.3 is associated with adverse risk in AML and MDS, is a potential therapeutic target, and is an attractive marker of measurable residual disease. High initial KMT2A-PTD RNA levels have been linked to poor prognosis, but mechanisms regulating KMT2A-PTD expression are not well understood. While it has been reported that KMT2A-PTD affects only a single allele, it has been theorized but not proven that duplications or genomic gains of a monoallelic KMT2A-PTD may occur, thereby potentially driving high expression and disease progression. Copy neutral loss of heterozygosity (CN-LOH) of 11q has also been described and is known to be associated with mutations in CBL but has not been reported to involve KMT2A-PTD. In this study, we identified 94 patients with KMT2A-PTDs using targeted DNA next-generation sequencing (NGS) and found that 16% (15/94) had complex secondary events, including CN-LOH and selective gain involving the KMT2A-PTD allele. High copy numbers indicating complexity were significantly enriched in AML versus MDS and correlated with higher RNA expression. Moreover, in serial samples, complexity was associated with relapse and secondary transformation. Taken together, we provide approaches to integrate quantitative and allelic assessment of KMT2A-PTDs into targeted DNA NGS and demonstrate that secondary genetic events occur in KMT2A-PTD by multiple mechanisms that may be linked to myeloid disease progression by driving increased expression from the affected allele.
Distinct representation of cue-outcome association by D1 and D2 neurons in the ventral striatum’s olfactory tubercle
Authors: Martiros Nuné , Kapoor Vikrant , Kim Spencer E. , Murthy Venkatesh N.
Published: November 2021

Positive and negative associations acquired through olfactory experience are thought to be especially strong and long-lasting. The conserved direct olfactory sensory input to the ventral striatal olfactory tubercle (OT) and its convergence with dense dopaminergic input to the OT could underlie this privileged form of associative memory, but how this process occurs is not well understood. We imaged the activity of the two canonical types of striatal neurons, expressing D1 or D2 type dopamine receptors, in the OT at cellular resolution while mice learned odor-outcome associations ranging from aversive to rewarding. D1 and D2 neurons both responded to rewarding and aversive odors. D1 neurons in the OT robustly and bidirectionally represented odor valence, responding similarly to odors predicting similar outcomes regardless of odor identity. This valence representation persisted even in the absence of a licking response to the odors and in the absence of the outcomes, indicating a true transformation of odor sensory information by D1 OT neurons. In contrast, D2 neuronal representation of the odor-outcome associations was weaker, contingent on a licking response by the mouse, and D2 neurons were more selective for odor identity than valence. Stimulus valence coding in the OT was modality-sensitive, with separate sets of D1 neurons responding to odors and sounds predicting the same outcomes, suggesting that integration of multimodal valence information happens downstream of the OT. Our results point to distinct representation of identity and valence of odor stimuli by D1 and D2 neurons in the OT.
Spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis
Authors: Lefrancq Noémie , Bouchez Valérie , Fernandes Nadia , Barkoff Alex-Mikael , Bosch Thijs , Dalby Tine , Åkerlund Thomas , Fabianova Katerina , Vestrheim Didrik F. , Fry Norman K. , González-López Juan José , Gullsby Karolina , Habington Adele , He Qiushui , Litt David , Martini Helena , Piérard Denis , Stefanelli Paola , Stegger Marc , Zavadilova Jana , Armatys Nathalie , Landier Annie , Guillot Sophie , Hong Samuel L. , Lemey Philippe , Parkhill Julian , Toubiana Julie , Cauchemez Simon , Salje Henrik , Brisse Sylvain
Published: November 2021

Competitive interactions between pathogen strains drive infection risk. Vaccines are thought to perturb strain diversity through shifts in immune pressures, however, this has rarely been measured due to inadequate data and analytical tools. Bordetella pertussis (B. pertussis), responsible for 160,000 deaths annually1, provides a rare natural experiment as many countries have switched from whole cell vaccines to acellular vaccines, which have very different immunogenic properties2,3. Here we use 3,344 sequences from 23 countries and build phylogenetic models to reveal that B. pertussis has substantial diversity within communities, with the relative fitness of local genotypes changing in response to switches in vaccine policy. We demonstrate that the number of transmission chains circulating within subnational regions is strongly associated with host population size. It takes 5-10 years for individual lineages to be homogeneously distributed throughout Europe or the United States. Increased fitness of pertactin-deficient strains following implementation of acellular vaccines, but reduced fitness otherwise, can explain long-term genotype dynamics. These findings highlight the role of national vaccine policies in shifting local diversity of a pathogen that still poses a large burden on global public health.
Targeted regulation of plasmid DNA expression in eukaryotic cells with a methylated-DNA-binding activator
Authors: Enwerem-Lackland Isioma , Warga Eric , Dugoni Margaret , Elmer Jacob , Haynes Karmella A.
Published: November 2021

Purpose: Targeted regulation of transfected extra-chromosomal plasmid DNA typically requires the integration of 9 - 20 bp docking sites into the plasmid. Here, we report an elegant approach, The Dpn Adaptor Linked Effector (DAL-E) system, to target fusion proteins to 6-methyladenosine in GATC, which appears frequently in popular eukaryotic expression vectors and is absent from endogenous genomic DNA. Methods: The DNA-binding region from the DpnI endonuclease binds 6-methyladenosine within the GATC motif. We used a Dpn-transcriptional activator (DPN7-TA) fusion to induce gene expression from transiently transfected pDNAs. Results: We validated methylation-dependent activity of DPN7-TA with a panel of target pDNAs. We observed stronger transactivation when GATC targets were located upstream of the transcriptional start site in the target pDNA. Conclusion: DAL-E, consisting of a 108 aa, 12 kD DNA-binding adaptor and a 4 bp recognition site, offers a genetically-tractable, tunable system that can potentially be redesigned to recruit a variety of regulators (e.g. activators, silencers, epigenome editors) to transfected plasmid DNA.
Transcriptional regulation of cyclophilin D by BMP/SMAD signaling and its role in osteogenic differentiation
Authors: Sautchuk Rubens , Kalicharan Brianna H , Escalera-Rivera Katherine , Jonason Jennifer H , Porter George A , Awad Hani , Eliseev Roman A
Published: November 2021

Cyclophilin D (CypD) promotes opening of the mitochondrial permeability transition pore (MPTP) which plays a key role in both cell physiology and pathology. It is, therefore beneficial for cells to tightly regulate CypD and MPTP but little is known about such regulation. We have reported before that CypD is downregulated and MPTP deactivated during differentiation in various tissues. Herein, we identify BMP/Smad signaling, a major driver of differentiation, as a transcriptional repressor of the CypD gene, Ppif. Using osteogenic induction of mesenchymal lineage cells as a model of BMP/Smad-dependent differentiation, we show that CypD is in fact transcriptionally repressed during this process. The importance of such CypD downregulation is evidenced by the negative effect of CypD ‘rescue’ via gain-of-function on osteogenesis both in vitro and in vivo. In sum, we characterized BMP/Smad signaling as a regulator of CypD expression and elucidated the role of CypD downregulation during cell differentiation.
Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs reveals that ribosome scans in a Brownian ratchet process
Authors: Li Ke , Kong Jinhui , Zhang Shuo , Zhao Tong , Qian Wenfeng
Published: November 2021

While eukaryotic ribosomes are widely presumed to scan mRNA for the AUG codon to initiate translation in a strictly 5′–3′ movement (strictly unidirectional scanning model), other evidence has suggested that the ribosome uses small-amplitude 5′–3′ and 3′–5′ oscillations with a net 5′–3′ movement to recognize the AUG codon (Brownian ratchet scanning model). Here, we generated 13,437 yeast variants, each with an ATG triplet placed downstream (dATGs) of the annotated ATG (aATG) codon of green fluorescent protein. We found that out-of-frame dATGs could inhibit translation at the aATG, but with diminishing strength over increasing distance between aATG and dATG, undetectable beyond ∼17 nt. Computational simulations revealed that each triplet is scanned back and forth approximately ∼10 times until an AUG codon is recognized. Collectively, our findings uncover the basic process by which eukaryotic ribosomes scan for initiation codons, and how this process could shape eukaryotic genome evolution and influence cancer development.
An essential ER-resident N-acetyltransferase in Plasmodium falciparum
Authors: Polino Alexander J , Floyd Katherine , Avila-Cruz Yolotzin , Yang Yujuan , Goldberg Daniel E.
Published: November 2021

N-terminal acetylation is a common eukaryotic protein modification that involves the addition of an acetyl group to the N-terminus of a polypeptide. This modification is largely performed by cytosolic N-terminal acetyltransferases (NATs). Most associate with the ribosome, acetylating nascent polypeptides co-translationally. In the malaria parasite Plasmodium falciparum, exported effectors are translated into the ER, processed by the aspartic protease plasmepsin V and then N-acetylated, despite having no clear access to cytosolic NATs. Here, we used post-transcriptional knockdown to investigate the most obvious candidate, Pf3D7_1437000. We found that it co-localizes with the ER-resident plasmepsin V and is required for parasite growth. However, depletion of Pf3D7_1437000 had no effect on protein export or acetylation of the exported proteins HRP2 and HRP3. Pf3D7_1437000-depleted parasites arrested later in their development cycle than export-blocked parasites, suggesting the protein’s essential role is distinct from protein export.
High-Speed Imaging Reveals the Bimodal Nature of Dense Core Vesicle Exocytosis
Authors: Zhang Pengcheng , Rumschitzki David , Edwards Robert H.
Published: November 2021

During exocytosis, the fusion of secretory vesicle with plasma membrane forms a pore that regulates release of neurotransmitter and peptide. Heterogeneity of fusion pore behavior has been attributed to stochastic variation in a common exocytic mechanism, implying a lack of biological control. Using a fluorescent false neurotransmitter (FFN), we imaged dense core vesicle (DCV) exocytosis in primary mouse adrenal chromaffin cells at millisecond resolution and observed strikingly divergent modes of release, with fast events lasting <30 ms and slow events persisting for seconds. Dual imaging of slow events shows a delay in the entry of external dye relative to FFN release, suggesting exclusion by an extremely narrow pore <1 nm in diameter. Unbiased comprehensive analysis shows that the observed variation cannot be explained by stochasticity alone, but rather involve distinct mechanisms, revealing the bimodal nature of DCV exocytosis. Further, loss of calcium sensor synaptotagmin 7 increases the proportion of slow events without changing the intrinsic properties of either class, indicating the potential for independent regulation. The identification of two distinct mechanisms for release capable of independent regulation suggests a biological basis for the diversity of fusion pore behavior.
Religiosity and stigmatization related to mental illness among African-Americans and Black immigrants: cross-sectional observational study and moderation analysis
Authors: Pederson Aderonke Bamgbose , Earnshaw Valerie A. , Lewis-Fernández Roberto , Hawkins Devan , Mangale Dorothy I. , Tsai Alexander C. , Thornicroft Graham
Published: November 2021

Objectives

Stigma about mental illness is a known barrier to engagement in mental health services. This study aimed to estimate the associations between religiosity and mental illness stigma among Black adults.

Design

We conducted an online cross-sectional study of Black adults in the United States (n=269, ages 18-65) from diverse ethnic backgrounds.

Results

Most (n=248 [92%]) participants attended religious services; while 21 (8%) never attended. Social distance was assessed as an index of past or current stigmatizing behavior. After adjusting for demographic factors, respondents with higher attendance at religious services or greater engagement in religious activities (e.g., prayer, meditation or Bible study) reported greater proximity to people living with mental health problems (RR=1.72; 95% CI: 1.14, 2.59 and RR=1.82; CI: 1.18, 2.79, respectively). Despite reporting greater past or current social proximity, respondents with higher religiosity indices also reported greater future intended stigmatizing behavior (or lower future intended social proximity) (RR’s=0.92-0.98). Ethnicity moderated the association between religiosity and future intended stigmatizing behavior. Black immigrants with higher religiosity reported lower future intended stigmatizing behavior (RR=1.16 CI: 1.02 – 1.32) whereas African-Americans with higher religiosity reported greater future intended stigmatizing behavior (RR = 0.83 CI: 0.76, 0.91).

Conclusions

Higher indices of religiosity were associated with lower past or current stigmatizing behavior towards individuals living with mental health problems but not lower future intended stigmatizing behavior. Focusing specifically on future intended stigmatizing behavior and the respondent’s level of religiosity, age, and ethnicity may be critical for designing effective stigma-reducing interventions for Black adults.
Plasmids as donors of Insertion Sequence elements mediating colistin resistance in Klebsiella pneumoniae
Authors: Fordham Stephen , Mantzouratou Anna , Sheridan Elizabeth Anne
Published: November 2021

Colistin is a last resort antibiotic for the treatment of carbapenemase producing Klebsiella pneumoniae (CRKP). In line with rising colistin use worldwide, colistin resistant Klebsiella pneumoniae (K. pneumoniae) isolates have emerged. The disruption of mgrB by insertion sequences (ISs) has been widely reported worldwide representing a mechanism mediating colistin resistance. Evidence suggests plasmids encode mobilizable IS elements which preferentially integrate into the mgrB gene in K. pneumoniae causing gene inactivation and colistin resistance.

Recognised IS elements targeting mgrB include ISL3 (ISKpn25), IS5 (ISKpn26), ISKpn14 and IS903B-like elements. K. pneumoniae represents the single largest species carrying plasmids encoding these IS elements. For IS presence among species, 1000 BLASTn hits were downloaded and filtered for plasmids. Additionally, the top 120 BLASTn non-duplicate circularised plasmid contig hits for each IS element were typed for incompatibility (Inc) group and carbapenemase gene presence.

IS903B was found in 28 unique Inc groups, while ISKpn25 was largely carried by IncFIB(pQil) plasmids. ISKpn26 and ISKpn14 were most often found associated with IncFII(pHN7A8) plasmids. Of the 34 unique countries which contained any of the IS elements, ISKpn25 was identified from 26. ISKpn26, ISKpn14, and IS903B insertion sequences were identified from 89.3%, 44.9% and 23.9% plasmid samples from China.

Plasmids carrying ISKpn25, ISKpn14, and ISKpn26 IS elements are 12.18, 27.0, and 44.43 times more likely to carry carbapenemase genes relative to plasmids carrying the IS element IS903B. Moreover, plasmids carrying ISKpn26, ISKpn25, and ISKpn14 were 6.10, 28.82, and 31.47 times more likely to be sourced from a clinical environmental setting than the environment relative to IS903B IS harboring plasmid.

ISKpn25 present on IncFIB(pQil) sourced from clinical settings is established across multiple countries, while ISKpn26, ISKpn14, and IS903B appear most often in China. High carbapenemase presence in tandem with IS elements may help promote an extensively drug resistant profile in K. pneumoniae limiting already narrow therapeutic treatment options.
Haspin participates in Aurora phosphorylation at centromeres and contributes to chromosome congression in male mouse meiosis
Authors: Berenguer I , López-Jiménez P , Mena I , Viera A , Page J , Maestre C , Malumbres M , Suja JA , Gómez R
Published: November 2021

Chromosome segregation requires that centromeres properly attach to spindle microtubules. This is an essential step towards the accuracy of cell division and therefore must be precisely regulated in both mitosis and meiosis. One of the main centromeric regulatory signaling pathways is the Haspin-H3T3ph-chromosomal passenger complex (CPC) cascade, which is responsible for the recruitment of the CPC to the centromeres. In mitosis, Haspin kinase phosphorylates H3 at threonine 3 (H3T3ph), the essential histone mark that recruits the CPC whose catalytic component is Aurora B kinase. To date, no data has yet been presented about the action of the centromeric Haspin-H3T3ph-CPC pathway in mammalian male meiosis. We have analyzed the consequences of Haspin chemical inhibition in cultured spermatocytes using LDN-192960. Ourin vitrostudies suggest that Haspin kinase activity is required for proper chromosome congression during both meiotic divisions and for the recruitment of phosphorylated Aurora B at meiotic centromeres. These results have been confirmed by the characterization of the meiotic phenotype of the genetic mouse modelHaspin-/-, which displays similar defects. In addition, our work demonstrates that the absence of H3T3ph histone mark does not alter SGO2 localization to meiotic centromeres. These results add new and relevant information regarding the regulation of centromere function during meiosis.
The ISOTILT software for discovering cooperative rigid-unit rotations in networks of interconnected rigid units
Authors: Campbell Branton J. , Stokes Harold T. , Averett Tyler B. , Machlus Shae , Yost Christopher J.
Published: November 2021

A user-friendly web-based software tool called `ISOTILT' is introduced for detecting cooperative rigid-unit modes (RUMs) in networks of interconnected rigid units (e.g. molecules, clusters or polyhedral units). This tool implements a recently described algorithm in which symmetry-mode patterns of pivot-atom rotation and displacement vectors are used to construct a linear system of equations whose null space consists entirely of RUMs. The symmetry modes are first separated into independent symmetry-mode blocks and the set of equations for each block is solved separately by singular value decomposition. ISOTILT is the newest member of the ISOTROPY Software Suite. Here, it is shown how to prepare structural and symmetry-mode information for use in ISOTILT, how to use each of ISOTILT's input fields and options, and how to use and interpret ISOTILT output.
Determination of the through-plane profile of vanadium species in hydrated Nafion studied with micro X-ray absorption near-edge structure spectroscopy – proof of concept
Authors: Lutz Christian , Hampel Sven , Beuermann Sabine , Turek Thomas , Kunz Ulrich , Garrevoet Jan , Falkenberg Gerald , Fittschen Ursula
Published: November 2021

Vanadium-ion transport through the polymer membrane results in a significant decrease in the capacity of vanadium redox flow batteries. It is assumed that five vanadium species are involved in this process. Micro X-ray absorption near-edge structure spectroscopy (micro-XANES) is a potent method to study chemical reactions during vanadium transport inside the membrane. In this work, protocols for micro-XANES measurements were developed to enable through-plane characterization of the vanadium species in Nafion 117 on beamline P06 of the PETRA III synchrotron radiation facility (DESY, Hamburg, Germany). A Kapton tube diffusion cell with a diameter of 3 mm was constructed. The tube diameter was chosen in order to accommodate laminar flow for cryogenic cooling while allowing easy handling of the cell components by hand. A vertical step size of 2.5 µm and a horizontal step size of 5 µm provided sufficient resolution to resolve the profile and good statistics after summing up horizontal rows of scan points. The beam was confined in the horizontal plane to account for the waviness of the membrane. The diffusion of vanadium ions during measurement was inhibited by the cryogenic cooling. Vanadium oxidation, e.g. by water radiolysis (water percentage in the hydrated membrane ∼23 wt%), was mitigated by the cryogenic cooling and by minimizing the dwell time per pixel to 5 ms. Thus, the photo-induced oxidation of V3+ in the focused beam could be limited to 10%. In diffusion experiments, Nafion inside the diffusion cell was exposed on one side to V3+ electrolyte and on the other side to VO2
+. The ions were allowed to diffuse across the through-plane orientation of the membrane during one of two short defrost times (200 s and 600 s). Subsequent micro-XANES measurements showed the formation of VO2+ from V3+ and VO2
+ inside the water body of Nafion. This result proves the suitability of the experimental setup as a powerful tool for the determination of the profile of vanadium species in Nafion and other ionomeric membranes.
Simultaneous two-color X-ray absorption spectroscopy using Laue crystals at an inverse-compton scattering X-ray facility
Authors: Huang Juanjuan , Günther Benedikt , Achterhold Klaus , Dierolf Martin , Pfeiffer Franz
Published: November 2021

X-ray absorption spectroscopy (XAS) is an element-selective technique that provides electronic and structural information of materials and reveals the essential mechanisms of the reactions involved. However, the technique is typically conducted at synchrotrons and usually only probes one element at a time. In this paper, a simultaneous two-color XAS setup at a laboratory-scale synchrotron facility is proposed based on inverse Compton scattering (ICS) at the Munich Compact Light Source (MuCLS), which is based on inverse Compton scattering (ICS). The setup utilizes two silicon crystals in a Laue geometry. A proof-of-principle experiment is presented where both silver (Ag) and palladium (Pd) K-edge X-ray absorption near-edge structure spectra were simultaneously measured. The simplicity of the setup facilitates its migration to other ICS facilities or maybe to other X-ray sources (e.g. a bending-magnet beamline). Such a setup has the potential to study reaction mechanisms and synergistic effects of chemical systems containing multiple elements of interest, such as a bimetallic catalyst system.