bluuebunny/crossref_metadata_2025 huggingface dataset:
Inactivity and Ca2+ signaling regulate synaptic compensation in motoneurons following hibernation in American bullfrogs
Authors: Zubov Tanya , do Amaral-Silva Lara , Santin Joseph M.
Published: January 2022

Neural networks tune synaptic and cellular properties to produce stable activity. One form of homeostatic regulation involves scaling the strength of synapses up or down in a global and multiplicative manner to oppose activity disturbances. In American bullfrogs, excitatory synapses scale up to regulate breathing motor function after inactivity in hibernation, connecting homeostatic compensation to motor behavior. In traditional models of homeostatic synaptic plasticity, inactivity is thought to increase synaptic strength via mechanisms that involve reduced Ca2+ influx through voltagegated channels. Therefore, we tested whether pharmacological inactivity and inhibition of voltage-gated Ca2+ channels are sufficient to drive synaptic compensation in this system. For this, we chronically exposed ex vivo brainstem preparations containing the intact respiratory network to tetrodotoxin (TTX) to stop activity and nimodipine to block L-type Ca2+ channels. We show that hibernation and TTX similarly increased motoneuron synaptic strength and that hibernation occluded the response to TTX. In contrast, block of L-type Ca2+ channels did not alter mean synaptic strength but disrupted the apparent multiplicative scaling of synaptic compensation typically observed in response to hibernation. Thus, inactivity drives up synaptic strength through mechanisms that do not rely on reduced L-type channel function, while Ca2+ signaling associated with the hibernation environment independently regulates the balance of synaptic weights. Altogether, these results point to multiple feedback signals for shaping synaptic compensation that gives rise to proper network function during environmental challenges in vivo.
Bio-inspired artificial printed bioelectronic cardio-3D-cellular constructs
Authors: Sanjuan-Alberte Paola , Whitehead Charlie , Jones Joshua N. , Silva João C. , Carter Nathan , Kellaway Simon , Hague Richard J.M. , Cabral Joaquim M.S. , Ferreira Frederico C. , White Lisa J. , Rawson Frankie J.
Published: January 2022

Bioelectronics is a growing field where novel smart materials are required to interface biology with electronic components. Conductive hydrogels have recently emerged as a promising material for biosensing/actuating applications as they can provide a wet, nanostructured and electrically conductive environment, minimising the mismatch between biological and electronic systems. In this work, we propose a strategy to develop conductive bioinks compatible with the freeform reversible embedding of suspended hydrogels (FRESH) extrusion bioprinting method. These bioinks are based on decellularized extracellular matrix (dECM), extracted from three different tissues (small intestine submucosa, liver and bone) and were characterised. 3D structures were manufactured containing human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs), exhibiting cell viabilities >80%. Multi-walled carbon nanotubes (MWCNTs) were selected as an additional component of the bioinks. The addition of the MWCNTs enhanced the conductive features of the hydrogels and the morphology of the dECM fibres. Electrical stimulation (ES) through alternating currents was applied to hPSC-CMs encapsulated in 3D structures manufactured with the previous material and our results indicated two main findings: (1) in the absence of external ES, the conductive properties of the materials can improve the contractile behaviour of the hPSC-CMs and (2) this effect is significantly enhanced under the application of external ES. Genetic markers analysed showed a trend towards a more mature state of the cells evaluated by the TNNI3/TNNI1 ratio, with upregulated SERCA2 and RYR2 calcium handling proteins when compared to controls and downregulation of calcium channels involved in the generation of pacemaking currents (CACNA1H). These results demonstrate the potential of our strategy to manufacture conductive hydrogels in complex geometries for bioactuating purposes. However, further development of the 3D bioprinting techniques is required to achieve higher control over the nano- and microarchitectures of the structures to improve their biomimicry.
Autolysis affects the iron cargo of ferritins in neurons and glial cells at different rates in the human brain
Authors: Sunkara Sowmya , Radulović Snježana , Lipovšek Saška , Birkl Christoph , Eggenreich Stefan , Birkl-Toeglhofer Anna Maria , Schinagl Maximilian , Funk Daniel , Stöger-Pollach Michael , Haybaeck Johannes , Goessler Walter , Ropele Stefan , Leitinger Gerd
Published: January 2022

Iron is known to accumulate in neurological disorders, so a careful balance of the iron concentration is essential for healthy brain functioning. An imbalance in iron homeostasis could arise due to the dysfunction of the proteins involved in iron homeostasis. Here, we focus on ferritin – the primary iron storage protein of the brain. Though it is known that glial cells and neurons differ in their concentration of ferritin, the change in the number of iron-filled ferritin cores or their distribution between different cell types during autolysis has not been revealed yet. Here, we show the cellular and region-wide distribution of ferritin in the human brain using state-of-the-art analytical electron microscopy. We validated the concentration of iron-filled ferritin cores to the absolute iron concentration measured by quantitative MRI and inductively coupled plasma mass spectrometry. We show that ferritins lost iron from their cores with progressing autolysis whereas the overall iron concentrations were unaffected. Though the highest concentration of ferritins was found in glial cells, we found that as the total ferritin concentration increased in a patient, ferritin accumulated more in neurons than in glial cells. Collectively our findings point out the unique behaviour of neurons in storing iron during autolysis and explain the differences between the absolute iron concentrations and iron-filled ferritin in a cell-type-dependent fashion in the human brain.

Significance statement

Balance of the iron load of the brain is crucial to preventing neurodegenerative disorders. Our study establishes a relation between autolysis, iron, and ferritin in the human brain with emphasis on the role of different cells in ferritin storage. We demonstrate that the iron load of ferritins does not correlate with mean iron concentrations during autolysis. Neurons retain more iron-loaded ferritin than glial cells with increasing ferritin count, which may make neurons more susceptible and exacerbate neuronal loss during iron overload. Neurons are also depleted of iron-loaded ferritin cores faster than glial cells during autolysis, demonstrating their unique role in iron storage. This paves the way to understanding the respective roles of neurons and glial cells in preventing or promoting neurodegeneration.
Upregulation ofTrem2expression occurs exclusively on microglial contact with plaques
Authors: Wood Jack , Wong Eugenia , Joghee Ridwaan , Balbaa Aya , Vitanova Karina S. , Vanshoiack Alison , Phelan Stefan-Laural J. , Launchbury Francesca , Desai Sneha , Tripathi Takshashila , Hanrieder Jörg , Cummings Damian M. , Hardy John , Edwards Frances A.
Published: January 2022

Using spatial cell-type-enriched transcriptomics, we compare plaque-induced gene (PIG) expression in microglia touching plaques, neighboring plaques, and far from plaques in 18-month-oldAPPNLF/NLFknock-in mice with and without the Alzheimer’s disease risk mutationTrem2R47H/R47H. We report that, inAppNLF/NLFmice, expression of 35/55 PIGs, is exclusively upregulated in microglia that are touching plaques. In 7 PIGs includingTrem2this upregulation is prevented by theTrem2R47H/R47Hmutation. Unlike in young mice, knockin of theTrem2R47H/R47Hmutation does not significantly decrease theTrem2expression but decreases protein levels by 20% in the absence of plaques. On plaques, despite the mutation preventing increased gene expression, TREM2 protein levels increased by 1.6-fold (compared to 3-fold withTrem2WT/WT) and microglial density increased 20-fold compared to 30-fold. Hence microglia must touch plaques beforeTrem2gene expression is increased but small changes in protein expression can increase microglia density without a change in gene expression.
Inhibitor of the nuclear transport protein XPO1 enhances the anticancer efficacy of KRAS G12C inhibitors in preclinical models of KRAS G12C mutant cancers
Authors: Khan Husain Yar , Nagasaka Misako , Li Yiwei , Aboukameel Amro , Uddin Md. Hafiz , Sexton Rachel , Bannoura Sahar , Mzannar Yousef , Al-Hallak Mohammed Najeeb , Kim Steve , Beydoun Rafic , Landesman Yosef , Mamdani Hirva , Uprety Dipesh , Philip Philip A. , Mohammad Ramzi M. , Shields Anthony F. , Azmi Asfar S.
Published: January 2022

The identification of molecules that can bind covalently to KRAS G12C and lock it in an inactive GDP-bound conformation has opened the door to targeting KRAS G12C selectively. These agents have shown promise in preclinical tumor models and clinical trials. FDA has recently granted approval to sotorasib for KRAS G12C mutated non-small cell lung cancer (NSCLC). However, patients receiving these agents as monotherapy may not respond and generally develop drug resistance over time. This necessitates the development of multi-targeted approaches that can potentially sensitize tumors to KRAS inhibitors. We generated KRAS G12C inhibitor-resistant cell lines and observed that they exhibit sensitivity toward selinexor, a selective inhibitor of nuclear export protein exportin1 (XPO1), as a single agent. KRAS G12C inhibitor MRTX1257 in combination with selinexor suppressed the proliferation of KRAS G12C mutant cancer cell lines MiaPaCa-2 and NCI-H2122 in a synergistic manner. Moreover, combined treatment of selinexor with KRAS G12C inhibitors resulted in enhanced spheroid disintegration, reduction in the number and size of colonies formed by G12C mutant cancer cells. A combination of selinexor with KRAS G12C inhibitors potentiated the inhibition of KRAS expression in MiaPaCa-2 cells. NF-kB protein expression was also markedly reduced by selinexor and MRTX1257 combination. In an in vivo KRAS G12C cell-derived xenograft model, oral administration of a combination of selinexor and sotorasib was demonstrated to reduce tumor burden and enhance survival. In conclusion, we have shown that the nuclear transport protein XPO1 inhibitor can enhance the anticancer activity of KRAS G12C inhibitors in preclinical cancer models.

Significance

In this study, combining nuclear transport inhibitor selinexor with KRAS G12C inhibitors has resulted in potent antitumor effects in preclinical cancer models. This can be an effective combination therapy for cancer patients that do not respond or develop resistance to KRAS G12C inhibitor treatment.
Recombination, selection and the evolution of tandem gene arrays
Authors: Otto Moritz , Zheng Yichen , Wiehe Thomas
Published: January 2022

Multi-gene families – immunity genes or sensory receptors, for instance – are often subject to diversifying selection. Allelic diversity may be favoured not only through balancing or frequency dependent selection at individual loci, but also by associating different alleles in multi copy gene families. Using a combination of analytical calculations and simulations, we explored a population genetic model of epistatic selection and unequal recombination, where a trade-off exists between the benefit of allelic diversity and the cost of copy abundance. Starting from the neutral case, where we showed that gene copy number is Gamma-distributed at equilibrium, we derived also mean and shape of the limiting distribution under selection. Considering a more general model which includes variable population size and population substructure, we explored by simulations mean fitness and some summary statistics of the copy number distribution. We determined the relative effects of selection, recombination and demographic parameters in maintaining allelic diversity and shaping mean fitness of a population. One way to control the variance of copy number is by lowering the rate of unequal recombination. Indeed, when encoding recombination by a rate modifier locus, we observe exactly this prediction. Finally, we analyzed the empirical copy number distribution of three genes in human and estimated recombination and selection parameters of our model.
KaiC-like proteins improve stress resistance in environmental Pseudomonas species
Authors: Terrettaz Céline , Cabete Bruno , Geiser Johan , Valentini Martina , Gonzalez Diego
Published: January 2022

KaiC is the central cog of the circadian clock in Cyanobacteria. Close homologs of this protein are widespread among bacteria that are not known to have or need a circadian physiology. The function, interaction network, and mechanism of action of these KaiC homologs are still largely unknown. Here, we focus on KaiC-like proteins found in environmental Pseudomonas species. Using a bioinformatic approach, we describe the diversity and distribution of members of this protein family in the Pseudomonas genus and sketch, through comparative genomics, a conserved minimal interaction network comprising a histidine kinase and a response regulator. We then characterize experimentally the only KaiC homolog present in Pseudomonas putida KT2440 and Pseudomonas protegens CHA0. Through phenotypic assays and transcriptomics, we show that KaiC is involved in osmotic and oxidative stress resistance in P. putida and in sulfur uptake and alternative carbon source utilization in P. protegens. As expected, it physically interacts with its cognate histidine kinase and response regulator. Moreover, KaiC homologs are phosphorylated at one (P. putida) or two (P. protegens) sites and KaiC phosphorylation patterns change over time; however, in Pseudomonas species, changes in KaiC phosphorylation are driven by the age of the culture rather than by circadian cues as is the case in Cyanobacteria. In this study, through thorough bioinformatic and experimental analyses, we shed light onto the functional diversification and evolution of a unique protein family, diversely involved in bacterial rhythmic interactions with their environment. By so doing, we present a striking example of a protein whose general purpose is conserved in evolution, but whose molecular mechanics and participation in bacterial physiology can change dramatically across species.
ARZIMM: A Novel Analytic Platform for the Inference of Microbial Interactions and Community Stability from Longitudinal Microbiome Study
Authors: He Linchen , Wang Chan , Hu Jiyuan , Gao Zhan , Falcone Emilia , Holland Steven , Blaser Martin J. , Li Huilin
Published: January 2022

Dynamic changes of microbiome communities may play important roles in human health and diseases. The recent rise in longitudinal microbiome studies calls for statistical methods that can model the temporal dynamic patterns and simultaneously quantify the microbial interactions and community stability. Here, we propose a novel autoregressive zero-inflated mixed-effects model (ARZIMM) to capture the sparse microbial interactions and estimate the community stability. ARZIMM employs a zero-inflated Poisson autoregressive model to model the excessive zero abundances and the non-zero abundances separately, a random effect to investigate the underlining dynamic pattern shared within the group, and a Lasso-type penalty to capture and estimate the sparse microbial interactions. Based on the estimated microbial interaction matrix, we further derive the estimate of community stability, and identify the core dynamic patterns through network inference. Through extensive simulation studies and real data analyses we evaluated ARZIMM in comparison with the other methods.
Multivalent interactions essential for lentiviral integrase function
Authors: Ballandras-Colas Allison , Chivukula Vidya , Gruszka Dominika T. , Shan Zelin , Singh Parmit K. , Pye Valerie E. , McLean Rebecca K. , Bedwell Gregory J. , Li Wen , Nans Andrea , Cook Nicola J. , Fadel Hind J. , Poeschla Eric M. , Griffiths David J. , Vargas Javier , Taylor Ian A. , Lyumkis Dmitry , Yardimci Hasan , Engelman Alan N. , Cherepanov Peter
Published: January 2022

A multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of the intasome from the maedi-visna virus (MVV), an ovine lentivirus, revealed a large assembly containing sixteen IN subunits (1). Herein, we report cryo-EM structures of the lentiviral intasome prior to engagement of target DNA and following strand transfer, refined at 3.4 and 3.5 Å resolution, respectively. The structures elucidate details of the protein-protein and protein-DNA interfaces involved in lentiviral intasome formation. We show that the homomeric interfaces involved in IN hexadecamer formation and the α-helical configuration of the linker connecting the C-terminal and catalytic core domains are critical for MVV IN strand transfer activity in vitro and for virus infectivity. Single-molecule microscopy in conjunction with photobleaching revealed that the MVV intasome can bind a variable number, up to sixteen molecules, of the lentivirus-specific host factor LEDGF/p75. Concordantly, ablation of endogenous LEDGF/p75 resulted in gross redistribution of MVV integration sites in human and ovine cells. Our data confirm the importance of the expanded architecture observed in cryo-EM studies of lentiviral intasomes and suggest that this organization underlies multivalent interactions with chromatin for integration targeting to active genes.
Convergent recruitment of Amh as the sex determination gene in two lineages of stickleback fish
Authors: Jeffries Daniel L. , Mee Jon , Peichel Catherine L.
Published: January 2022

Sex chromosomes vary greatly in their age and levels of differentiation across the tree of life. This variation is largely due to the rates of sex chromosome turnover in different lineages; however, we still lack an explanation for why sex chromosomes are so conserved in some lineages (e.g. Mammals, Birds) but so labile in others (e.g. Fish, Amphibians). Here we add to the information on sex chromosomes in stickleback, a valuable model lineage for the study of sex chromosome evolution, by identifying the sex chromosome and a strong candidate for the master sex determination gene in the brook stickleback, Culaea inconstans. Using whole genome sequencing of wild-caught samples and a lab cross, we identify AmhY, a male specific duplication of the gene Amh, as the candidate master sex determination gene. AmhY resides on Chromosome 20 in C. inconstans and is likely a recent duplication, as both AmhY and the sex linked region of Chromosome 20 show little sequence divergence. Importantly, this duplicate AmhY represents the second independent duplication and recruitment of Amh as the sex determination gene in stickleback and the eighth example now known across teleosts. We discuss this convergence in the context of sex chromosome turnovers and the role that the Amh/AmhrII pathway, which is crucial for sex determination, may play in the evolution of sex chromosomes in teleosts.
Marine Bacteria Chemotaxis to Crude Oil Components with Opposing Effects
Authors: Zhao Xueying , Ford Roseanne M.
Published: January 2022

Marine microorganisms were critical to hydrocarbon removal from the Gulf of Mexico oil spill. Chemotaxis, a process attracting motile bacteria toward higher hydrocarbon concentrations, can increase biodegradation efficiency. However, crude oil also contains heavy metal ions that repel bacteria. Will bacteria migrate toward hydrocarbons or away from heavy metals? We exposed a marine isolate Halomonas sp. to decane and copper ions in a microfluidic device that maintained a constant concentration gradient across a channel. Bacterial distributions were used to quantify parameters in a mathematical model capturing bacteria motility and chemotaxis. This multi-scale model was adapted from the signal transduction mechanism of E. coli. For Halomonas sp., we used independent receptors for sensing attractant or repellent and chemotaxis parameter values were assessed. Predictions based on the multi-scale model correctly estimated the net attraction or repulsion responses of bacteria to the stimuli mixture. In some cases, the model yielded a stronger repulsion than what was observed experimentally, but still captured the general trends of bacteria distribution. Understanding how marine bacteria integrate information from multiple inputs to yield net migration toward or away from oil will improve predictions of hydrocarbon degradation rates.
T-lymphocyte Tyrosine Hydroxylase Regulates TH17 T-lymphocytes during Repeated Social Defeat Stress
Authors: Elkhatib Safwan K. , Moshfegh Cassandra M. , Watson Gabrielle F. , Case Adam J.
Published: January 2022

Posttraumatic stress disorder (PTSD) is a debilitating psychiatric disorder which results in deleterious changes to psychological and physical health. Patients with PTSD are especially susceptible to co-morbid inflammation-driven pathologies, such as autoimmunity, while also demonstrating increased T-helper 17 (TH17) lymphocyte-driven inflammation. While the exact mechanism of this increased inflammation is unknown, overactivity of the sympathetic nervous system is a hallmark of PTSD. Neurotransmitters of the sympathetic nervous system (i.e., catecholamines) can alter T-lymphocyte function, which we have previously demonstrated to be partially mitochondrial redox-mediated. Furthermore, we have previously elucidated that T-lymphocytes generate their own catecholamines, and strong associations exist between tyrosine hydroxylase (TH; the rate-limiting enzyme in the synthesis of catecholamines) and pro-inflammatory interleukin 17A (IL-17A) expression within purified T-lymphocytes in a preclinical rodent model of PTSD. Therefore, we hypothesized that T-lymphocyte-generated catecholamines drive TH17 T-lymphocyte polarization through a mitochondrial superoxide-dependent mechanism during psychological trauma. To test this, T-lymphocyte-specific TH knockout mice (THT-KO) were subjected to repeated social defeat stress (RSDS). RSDS characteristically increased tumor necrosis factor-α (TNFα), IL-6, IL-17A, and IL-22, however, IL-17A and IL-22 (TH17 produced cytokines) were selectively attenuated in circulation and in T-lymphocytes of THT-KO animals. When activated ex vivo, secretion of IL-17A and IL-22 by THT-KO T-lymphocytes was also found to be reduced, but could be partially rescued with supplementation of norepinephrine specifically. Interestingly, THT-KO T-lymphocytes were still able to polarize to TH17 under exogenous polarizing conditions. Last, contrary to our hypothesis, we found RSDS-exposed THT-KO T-lymphocytes still displayed elevated mitochondrial superoxide, suggesting increased mitochondrial superoxide is upstream of T-lymphocyte TH induction, activity, and TH17 regulation. Overall, these data demonstrate TH in T-lymphocytes plays a critical role in RSDS-induced TH17 T-lymphocytes and offer a previously undescribed regulator of inflammation in RSDS.
The IMD and JNK pathways drive the functional integration of the immune and circulatory systems of mosquitoes
Authors: Yan Yan , Sigle Leah T. , Rinker David C. , Estévez-Lao Tania Y. , Capra John A. , Hillyer Julián F.
Published: January 2022

The immune and circulatory systems of animals are functionally integrated. In mammals, the spleen and lymph nodes filter and destroy microbes circulating in the blood and lymph, respectively. In insects, immune cells that surround the heart valves (ostia), called periostial hemocytes, destroy pathogens in the areas of the body that experience the swiftest hemolymph (blood) flow. An infection recruits additional periostial hemocytes, amplifying heart-associated immune responses. Although the structural mechanics of periostial hemocyte aggregation have been defined, the genetic factors that regulate this process remain less understood. Here, we conducted RNAseq in the African malaria mosquito, Anopheles gambiae, and discovered that an infection upregulates multiple components of the IMD and JNK pathways in the heart with periostial hemocytes. This upregulation is greater in the heart with periostial hemocytes than in the circulating hemocytes or the entire abdomen. RNAi-based knockdown then showed that the IMD and JNK pathways drive periostial hemocyte aggregation and alter phagocytosis and melanization on the heart, thereby demonstrating that these pathways regulate the functional integration between the immune and circulatory systems. Understanding how insects fight infection lays the foundation for novel strategies that could protect beneficial insects and harm detrimental ones.
Structural and mechanistic insights into the MCM8/9 helicase complex
Authors: Weng Zhuangfeng , Zheng Jiefu , Zhou Yiyi , Lu Zuer , Wu Yixi , Xu Dongyi , Li Huanhuan , Liang Huanhuan , Liu Yingfang
Published: January 2022

MCM8 and MCM9 form a functional helicase complex (MCM8/9) that plays an essential role in DNA homologous recombination repair for DNA double-strand break. However, the structural characterization of MCM8/9 for DNA binding/unwinding remains unclear. Here, we report structures of the MCM8/9 complex using cryo-electron microscopy single particle analysis. The structures reveal that MCM8/9 is arranged into a heterohexamer through a three-fold symmetry axis, creating a central channel that accommodates DNA. Multiple characteristic hairpins from the N-terminal oligosaccharide/oligonucleotide (OB) domains of MCM8/9 protrude into the central channel and serve to unwind the duplex DNA. When activated by HROB, the structure of MCM8/9’s N-tier ring converts its symmetry fromC3toC1with a conformational change that expands the MCM8/9’s trimer interface. Moreover, our structural dynamic analyses revealed that the flexible C-tier ring exhibited rotary motions relative to the N-tier ring, which is required for the unwinding ability of MCM8/9. In summary, our structural and biochemistry study provide a basis for understanding the DNA unwinding mechanism of MCM8/9 helicase in homologous recombination.
Methacrylate-Modified Gold Nanoparticles Enable Non-Invasive Monitoring of Photocrosslinked Hydrogel Scaffolds
Authors: Li Lan , Gil Carmen J. , Finamore Tyler A. , Evans Connor J. , Tomov Martin L. , Ning Liqun , Theus Andrea , Kabboul Gabriella , Serpooshan Vahid , Roeder Ryan K.
Published: January 2022

Photocrosslinked hydrogels, such as methacrylate-modified gelatin (gelMA) and hyaluronic acid (HAMA), are widely utilized as tissue engineering scaffolds and/or drug delivery vehicles, but lack a suitable means for non-invasive, longitudinal monitoring of surgical placement, biodegradation, and drug release. Therefore, we developed a novel photopolymerizable X-ray contrast agent, methacrylate-modified gold nanoparticles (AuMA NPs), to enable covalent-linking to methacrylate-modified hydrogels (gelMA and HAMA) in one-step during photocrosslinking and non-invasive monitoring by X-ray micro-computed tomography (micro-CT). Hydrogels exhibited a linear increase in X-ray attenuation with increased Au NP concentration to enable quantitative imaging by contrast-enhanced micro-CT. The enzymatic and hydrolytic degradation kinetics of gelMA-Au NP hydrogels were longitudinally monitored by micro-CT for up to one monthin vitro, yielding results that were consistent with concurrent measurements by optical spectroscopy and gravimetric analysis. Importantly, AuMA NPs did not disrupt the hydrogel network, rheology, mechanical properties, and hydrolytic stability compared with gelMA alone. GelMA-Au NP hydrogels were thus able to be bioprinted into well-defined three-dimensional architectures supporting endothelial cell viability and growth. Overall, AuMA NPs enabled the preparation of both conventional photopolymerized hydrogels and bioprinted scaffolds with tunable X-ray contrast for noninvasive, longitudinal monitoring of placement, degradation, and NP release by micro-CT.
Detection of SARS-CoV-2 Omicron, Delta, Alpha and Gamma variants using a rapid antigen test
Authors: Salcedo Nol , Nandu Nidhi , Boucau Julie , Herrera Bobby Brooke
Published: January 2022

Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged with different infection and disease dynamics. Testing strategies, including clinical diagnosis, surveillance, and screening, have been deployed to help limit the spread of SARS-CoV-2 variants. Rapid antigen tests, in particular, have been approved for self-testing in many countries and governments are supporting their manufacturing and distribution. However, studies demonstrating the accuracy of rapid antigen tests in detecting SARS-CoV-2 variants, especially the new Omicron variant, are limited. We determined the analytical sensitivity of a CE-marked rapid antigen test against the Omicron, Delta, Alpha and Gamma variants. The rapid antigen test had the most sensitive limit of detection (10 plaque forming units [PFU]/mL) when tested with the Alpha and Gamma variants, followed by the Omicron (100 PFU/mL) and Delta (1,000 PFU/mL) variants. Given the increasing numbers of breakthrough infections and the need to surveil infectiousness, rapid antigen tests are effective public health tools to detect SARS-CoV-2 variants.
Large Registry Based Analysis of Genetic Predisposition to Tuberculosis Identifies Genetic Risk Factors at HLA
Authors: Tervi Anniina , Junna Nella , Broberg Martin , Jones Samuel E. , FinnGen  , Strausz Satu , Kreivi Hanna-Riikka , Heckman Caroline A. , Ollila Hanna M.
Published: January 2022

Tuberculosis is a significant public health concern resulting in the death of over 1 million individuals each year worldwide. While treatment options and vaccines exist, a substantial number of infections still remain untreated or are caused by treatment resistant strains. Therefore, it is important to identify mechanisms that contribute to risk and prognosis of tuberculosis as this may provide tools to understand disease mechanisms and provide novel treatment options for those with severe infection. Our goal was to identify genetic risk factors that contribute to the risk of tuberculosis and to understand biological mechanisms and causality behind the risk of tuberculosis. A total of 1,895 individuals in the FinnGen study had ICD-based tuberculosis diagnosis. GWAS analysis identified genetic variants with statistically significant association with tuberculosis at the Human leukocyte antigen (HLA) region (p<5e-8) and at rs560595454 in gene INPP5A. Fine mapping the HLA-association provided evidence for one protective haplotype tagged by HLA DQB1*05:01 (p=1.82E-06, OR = 0.81 [CI 95 % 0.74-0.88]), and predisposing alleles tagged by HLA DRB1*13:02 (p=0.00011, OR = 1.35 [CI 95% 1.16-1.57]). Furthermore, genetic correlation analysis showed association with earlier reported risk factors including smoking (p<0.05). Mendelian randomization supported smoking as a risk factor for tuberculosis (inverse-variance weighted p<0.05, OR = 1.83 [CI 95 % 1.15-2.93]) with no significant evidence of pleiotropy. Our findings indicate that specific HLA alleles and INPP5A associate with the risk of tuberculosis. In addition, lifestyle risk factors such as smoking contribute to the risk of developing tuberculosis.
Generation of stable microtubule superstructures by binding of peptide-fused tetrameric proteins to inside and outside
Authors: Inaba Hiroshi , Sueki Yurina , Ichikawa Muneyoshi , Kabir Arif Md. Rashedul , Iwasaki Takashi , Shigematsu Hideki , Kakugo Akira , Sada Kazuki , Matsuura Kazunori
Published: January 2022

Microtubules (MTs) play important roles in biological functions by forming superstructures, such as doublets, triplets, and branched structures, in vivo. Formation of these superstructures by exogenous molecules in vitro will be useful not only for understanding the functions of MTs but also as components of MT-based nanomaterials. Here, we developed a tetrameric fluorescent protein Azami-Green (AG) fused with a His-tag and Tau-derived peptide (TP), TP–AG, which can bind to the inside or outside of MTs depending on the polymerization conditions. The binding of TP–AG to the inside of MTs induced the formation, stabilized, and increased the rigidity of the MTs. The binding of TP–AG to the outside of MTs induced various types of MT superstructures, including doublets, multiplets, and branched structures, by recruiting tubulins to MTs. The formation of motile MT aster structures by TP–AG was also observed. The generation of MT superstructures by these exogenous proteins provides guidelines for the design of MT-based nanomaterials.
PfD123 modulates K13-mediated survival and recovery after artemisinin exposure
Authors: Nötzel Christopher , Kafsack Björn F. C.
Published: January 2022

Recent advances in curbing the deadly toll of malaria have been threatened by the emergence of parasites resistant to the front-line antimalarial artemisinin. Resistance is mediated by point-mutations in the parasite protein Kelch13, but the mechanism of resistance is multi-factorial and only partially understood. Resistance-conferring Kelch13 mutations have been shown to lead to low-level activation of the parasite’s integrated stress response (ISR) which has a protective effect against artemisinin through an unclear mechanism. Furthermore, only a subpopulation of resistant parasites ever survives drug exposure, implying an underlying heterogeneity. By applying scRNAseq to the resistance-relevant early ring stage, we found expansion of a subpopulation in Kelch13 mutant parasites that is chiefly characterized by transcription of the putative positive translational regulator D123, while we conversely observed reduced D123 protein levels at the same stage. Analogous inverse changes in D123 expression are produced by experimental activation of the ISR, and genetically manipulating D123 expression modulates sensitivity to artemisinin, establishing it as a stress-responsive gene that contributes to artemisinin resistance in Kelch13-mutant malaria parasites.
Transcription factor FOXM1 specifies the loading of chromatin DNA to extracellular vesicles
Authors: Zhang Yunsheng , Ding Nana , Li Yizhen , Zhao Xiaoyun , Yang Shiping , Fu Ping , Peng Yousong , Cheng Haojie , Ouyang Min , Wang Ruiping , Wang Yu , Liu Hanyun , Chen Yan , Huang Xiaoqin , Yu Li , Tan Yongjun
Published: January 2022

Extracellular vesicle DNAs (evDNAs) possess the important diagnostic value for multiple diseases and play roles for horizontally transferring genetic materials among cells. In this study, we have found that transcription factor FOXM1 can mediate the loading of certain chromatin genes or DNA fragments (named FOXM1-chDNAs) to extracellular vesicles (EVs). FOXM1 interacts with LC3 in nucleus and FOXM1-chDNAs (such asDUX4gene and Telomere DNA) are specified by FOXM1 and translocated to cytoplasm. These DNAs are released to EVs through the process of an LC3-involved autophagosome-multivesicular body (MVB) transport. The roles of FOXM1 on loading FOXM1-chDNAs to EVs are further confirmed by DNA-FISH experiments, tracing the translocation of selected chromatin loci with the TetO/TetR-GFP method, and PCR analysis of the DNA samples from MVBs and EVs. Furthermore, disrupting the expression of FOXM1 or the process of autophagosome-MVB transport impairs the loading of FOXM1-chDNAs to EVs. This discovery suggests that transcription factor FOXM1 contributes the constitution of evDNAs from nuclear chromatin, providing the first example to explain how chromatin DNA fragments are specified and loaded to EVs. It also provide a foundation to further explore the roles of evDNAs in biological processes such as the horizontal gene transfer.
An Optimal Regulation of Fluxes Dictates Microbial Growth In and Out of Steady-State
Authors: Chure Griffin , Cremer Jonas
Published: January 2022

Effective coordination of cellular processes is critical to ensure the competitive growth of microbial organisms. Pivotal to this coordination is the appropriate partitioning of cellular resources between protein synthesis via translation and the metabolism needed to sustain it. Here, we extend a low-dimensional allocation model to describe the dynamic control of this resource partitioning. At the core of this regulation is the optimal coordination of metabolic and translational fluxes, mechanistically achieved via the perception of charged- and uncharged-tRNA turnover. An extensive comparison with ≈ 60 data sets fromEscherichia coliestablishes this regulatory mechanism’s biological veracity and demonstrates that a remarkably wide range of growth phenomena in and out of steady state can be predicted with quantitative accuracy. This predictive power, achieved with only a few biological parameters, cements the preeminent importance of optimal flux regulation across conditions and establishes low-dimensional allocation models as an ideal physiological framework to interrogate the dynamics of growth, competition, and adaptation in complex and ever-changing environments.
Development of DNA methylation-based epigenetic age predictors in loblolly pine (Pinus taeda)
Authors: Gardner Steven T. , Bertucci Emily M. , Sutton Randall , Horcher Andy , Aubrey Doug , Parrott Benjamin B.
Published: January 2022

Biological aging is connected to life history variation across ecological scales, as well as informing a basic understanding of age-related declines to organismal function. Altered DNA methylation dynamics are a conserved aspect of biological aging and have recently been modeled to predict chronological age among vertebrate species. In addition to their utility in estimating individual age, differences between chronological and predicted ages arise due to acceleration or deceleration of epigenetic aging, and these discrepancies are linked to disease risk and multiple life history traits. Although evidence suggests that patterns of DNA methylation can describe aging in plants, predictions with epigenetic clocks have yet to be performed. Here, we resolve the DNA methylome across CpG, CHG, and CHH-methylation contexts in the loblolly pine tree (Pinus taeda) and construct epigenetic clocks capable of predicting ages in this species within 8% of its lifespan. Although patterns of CHH methylation showed little association with age, both CpG and CHG methylation contexts were strongly associated with aging, largely becoming hypomethylated with age. Among age-associated loci were those in close proximity to malate dehydrogenase, NADH dehydrogenase, and 18S and 26S ribosomal RNA genes. This study reports one of the first epigenetic clocks in plants and demonstrates the universality of age-associated DNA methylation dynamics which can inform conservation and management practices, as well as our ecological and evolutionary understanding of biological aging in plants.
A novel bacteriocin produced byBifidobacterium longumsubsp.infantishas dual antimicrobial and immunomodulatory activity
Authors: Javvadi Sree Gowrinadh , Kujawska Magdalena , Papp Diana , Gontarczyk Aleksander M , Jordan Anne , Lawson Melissa A.E. , O’Neill Ian J. , Alcon-Giner Cristina , Kiu Raymond , Clarke Paul , Beraza Naiara , Hall Lindsay J
Published: January 2022

Bacteriocins are ribosomally-synthesized antimicrobial peptides produced by bacteria with either narrow or broad spectrum activity. Many genome mining studies have indicated that bacteriocin gene clusters are widespread within certain gut microbiota members. In early life,Bifidobacteriumcomprise the dominant microbiota genus in vaginally delivered and breast-fed infants, with high levels associated with improved health. However, in many cases the mechanisms underlying these beneficial effects are unknown, although a limited number of studies have suggested that bacteriocin production byBifidobacteriummay represent a key mechanism for preventing pathogen over-growth. Here, we used BAGEL4 and antiSMASH to identify putative bacteriocin sequences in the whole genome sequences of 33Bifidobacteriumstrains isolated from infants participating in two clinical studies. We identified a novel non-lantibiotic bacteriocin fromBifidobacterium longumsubsp.infantisLH_664, with 40% sequence homology to Lactococcin 972 fromLactococcus lactissubsp.lactis. The putative bacteriocin (Bifidococcin_664) was chemically synthesized and studied for antimicrobial and immune-modulatory activities. We determined it has discrete activity againstClostridium perfringensand it appears to have novel immune stimulatory activities, promoting macrophage phagocytosis and specific cytokine release. These data highlight strain-specific beneficial properties in the early life genusBifidobacterium, and suggest avenues for development of novel and highly specific dual action antimicrobials, and possible probiotic strains, that are active against clinically important bacterial pathogens.

Data summary

Samples LH_9 to LH_666 were previously sequenced and deposited to ENA under accession numbers ERS2658025-ERS2658043. Samples LH_986 to LH_1052 are newly sequenced and deposited to NCBI under accession numbers SAMN24838598-SAMN24838611. Additionally, previously assembled publicly available sequences (n=7) were retrieved online from NCBI Genomes database. See Supplementary Table S1 for further details.
Genetic characterization of ABC pesticide transporters establishes Drosophila as an in vivo model for toxicogenetics
Authors: Denecke Shane , Lương Hằng Ngọc Bao , Koidou Venetia , Kalogeridi Maria , Socratous Rafaella , Howe Steven , Vogelsang Kathrin , Nauen Ralf , Batterham Phil , Geibel Sven , Vontas John
Published: January 2022

Pesticides remain one of the most effective ways of controlling agricultural and public health insects, but much is still unknown regarding how these compounds reach their targets. Specifically, the role of ABC transporters in pesticide absorption and excretion is poorly understood, especially compared to the detailed knowledge in mammalian systems. Here, we present a comprehensive characterization of pesticide transporters in the model insect D. melanogaster. An RNAi screen was performed, which knocked down individual ABCs in targeted epithelial tissue, examining the subsequent changes in sensitivity to the pesticides spinosad and fipronil. This simultaneously implicated a novel ABC drug transporter CG4562 but also highlighted a predominant role for the P-glycoprotein orthologue Mdr65. Further characterization of the P-glycoprotein family was performed via transgenic overexpression and immunolocalization, finding that Mdr49 and Mdr50 play enigmatic roles in pesticide toxicology perhaps determined by their different subcellular localizations within the midgut. Lastly, heterologous expression of the Mdr65 orthologue from the major malaria vector Anopheles gambiae was used to establish an in vivo characterization system for the characterization of P-glycoproteins from non-model insects in D. melanogaster. This study provides the basis for establishing Drosophila as a model for toxicology research regarding drug transporters.
Acute Axon Damage and Demyelination are Mitigated by 4-Aminopyridine (4-AP) Therapy after Experimental Traumatic Brain Injury
Authors: Radomski Kryslaine L. , Zi Xiaomei , Lischka Fritz W. , Noble Mark D. , Galdzicki Zygmunt , Armstrong Regina C.
Published: January 2022

Damage to long axons in white matter tracts is a major pathology in closed head traumatic brain injury (TBI). Acute TBI treatments are needed that protect against axon damage and promote recovery of axon function to prevent long term symptoms and neurodegeneration. Our prior characterization of axon damage and demyelination after TBI led us to examine repurposing of 4-aminopyridine (4-AP), an FDA-approved inhibitor of voltage-gated potassium (Kv) channels. 4-AP is currently indicated to provide symptomatic relief for patients with chronic stage multiple sclerosis, which involves axon damage and demyelination. We tested clinically relevant dosage of 4-AP as an acute treatment for experimental TBI and found multiple benefits in corpus callosum axons. This randomized, controlled pre-clinical study focused on the first week after TBI, when axons are particularly vulnerable. 4-AP treatment initiated one day post-injury dramatically reduced axon damage detected by intra-axonal fluorescence accumulations in Thy1-YFP mice of both sexes. Detailed electron microscopy in C57BL/6 mice showed that 4-AP reduced pathological features of mitochondrial swelling, cytoskeletal disruption, and demyelination. Furthermore, 4-AP improved the molecular organization of axon nodal regions by restoring disrupted paranode domains and reducing Kv1.2 channel dispersion. 4-AP treatment did not resolve deficits in action potential conduction across the corpus callosum, based on ex vivo electrophysiological recordings at 7 days post-TBI. Thus, this first study of repurposing 4-AP as an acute treatment for TBI demonstrates pre-clinical efficacy in decreasing pathological hallmarks of axon damage. Studies beyond this acute phase are now warranted to assess functional utility and outcome trajectory.

SIGNIFICANCE STATEMENT

Traumatic brain injury (TBI) is an acute injury that, if unresolved, can progress to cause persistent, debilitating symptoms. Currently, no treatments effectively prevent damage to long myelinated axons in white matter tracts, which is a hallmark pathology of TBI. 4-aminopyridine (4-AP) is FDA-approved to treat chronic symptoms in patients with multiple sclerosis, which involves autoimmune damage to myelinated axons. As the first assessment of repurposing 4-AP as an acute treatment for TBI, our randomized, controlled studies tested the hypothesis that low-dose 4-AP initiated one day after experimental TBI will reduce acute axon damage and demyelination. We found that 4-AP treatment significantly reduced the progression of axon pathology and demyelination during the first week after TBI using clinically relevant experimental conditions.
Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes
Authors: Ito Yosuke , Chadani Yuhei , Niwa Tatsuya , Yamakawa Ayako , Machida Kodai , Imataka Hiroaki , Taguchi Hideki
Published: January 2022

Robust translation elongation of any given amino acid sequence is a prerequisite to shape proteomes. Nevertheless, nascent peptides could destabilize ribosomes, since consecutive negatively charged residues in bacterial nascent chains stochastically can induce discontinuation of translation, in a phenomenon termed intrinsic ribosome destabilization (IRD). Here, we show that IRD also occurs in eukaryotic translation. Nascent chains enriched in aspartic acid (D) or glutamic acid (E) in the N-terminal regions could prematurely terminate translation, producing premature products as peptidyl-tRNA species. Although eukaryotic ribosomes are more robust to ensure uninterrupted translation, we found many endogenous D/E-rich peptidyl-tRNAs in the N-terminal regions in cells lacking a peptidyl-tRNA hydrolase, indicating that the translation of the N-terminal D/E-rich sequences poses an inherent risk. Indeed, a bioinformatics analysis revealed that the N-terminal regions of ORFs avoid D/E enrichment, implying that the translation defect partly restricts the overall amino acid usage in proteomes.