bluuebunny/crossref_metadata_2025 huggingface dataset:
An alternative tetrahydrofolate pathway for formaldehyde oxidation in verrucomicrobial methanotrophs: Primer design for folD and ftfL and transformation of E. coli
Authors: Schmitz Rob A. , Pelsma Koen A.J. , Op den Camp Huub J.M.
Published: August 2022

Methylotrophs make a living by using one-carbon compounds as energy and carbon source. Methanol (CH3OH) is utilized by various methylotrophs and is oxidized by a methanol dehydrogenase. The calcium-dependent methanol dehydrogenase MxaFI converts methanol to formaldehyde (CH2O). In addition to MxaFI, the lanthanide-dependent methanol dehydrogenase XoxF is found in a wide range of bacteria. XoxF isolated from the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV possesses an unusually high affinity for both methanol and formaldehyde and converts methanol to formate (HCOOH) in vitro. However, genomic analyses and biochemical studies on related XoxF methanol dehydrogenases have questioned whether these enzymes are dedicated to the conversion of formaldehyde to formate in vivo. Instead, the genes encoding the bifunctional enzyme FolD and the enzyme FtfL, which we detected in all verrucomicrobial methanotrophs, were proposed to form a formaldehyde oxidation pathway utilizing tetrahydrofolate as C1-carrier. folD and ftfL are expressed in M. fumariolicum SolV and most closely related to homologues found in the phyla Verrucomicrobia and Proteobacteria, respectively. Here, we designed primers targeting Mf-folD and Mf-ftfL and amplified these genes through PCR. The amplified genes were ligated into pET30a(+) vectors which were subsequently used for the successful transformation of E. coli XL1-Blue cells. The vectors can be used for heterologous expression and subsequent His-tag purification to biochemically investigate whether FolD and FtfL could form an alternative tetrahydrofolate pathway for formaldehyde oxidation in verrucomicrobial methanotrophs.
Identification of potential biomarker candidates of drug-induced vascular injury (DIVI) in rats using gene expression and histopathology data
Authors: Liu Anika , Munoz-Muriedas Jordi , Bender Andreas , Dalmas Deidre A.
Published: August 2022

Drug-induced vascular injury (DIVI) observed in non-clinical species often leads to significant delays or termination of compounds in drug development due to the lack of translatable biomarkers and unknown relevance to humans. This study focused on the identification of potential biomarker candidates of drug-induced vascular injury, or more specifically mesenteric medial arterial necrosis (MAN), in rats. To do so, an adapted bioinformatic filtering pipeline was applied to previously generated gene expression data obtained from laser capture microdissected endothelial and vascular smooth muscle cells and corresponding histopathological annotations from mesenteric arteries following treatment of rats with known vascular toxicants, non-vasotoxic vasoactive comparator compounds, and corresponding vehicle. A novel gene panel including 33 genes with consistent, specific, and dose-responsive dysregulation across multiple treatments inducing MAN was identified. The degree to which these reflect injury progression was characterized and changes were identified in samples from animals where injury was anticipated but not yet histologically observed. The most predictive candidates (AUC > 0.9) with the strongest changes (logFC > 1.7) in MAN encode secreted proteins (Tnc, Vcan, Timp1andFn1)which are strongly interlinked with each other and other potential candidate biomarkers encoding cell surface proteins. Although further validation is required for biomarker qualification, the adapted bioinformatic approach utilized in this study provides informed data-driven starting points for further DIVI biomarker discovery and development in rats, as well as potential mechanistic insight into MAN pathogenesis.
Rewiring cattle movements to limit infection spread
Authors: Morel-Journel Thibaut , Ezanno Pauline , Vergu Elisabeta
Published: August 2022

The cattle tracing databases set up over the past decades in Europe have become major resources for representing demographic processes of livestock and assessing potential risk of infections spreading by trade. The herds registered in these databases are nodes of a network of commercial movements, which can be altered to lower the risk of disease transmission. In this study, we develop an algorithm aimed at reducing the number of infected animals and herds, by rewiring specific movements responsible for trade flows from high- to low-prevalence herds. The algorithm is coupled with a generic computational model describing infection spread within and between herds, based on data extracted from the French cattle movement tracing database (BDNI). This model is used to simulate a wide array of infections, with either a recent outbreak (epidemic) or an outbreak that occurred five years earlier (endemic), on which the performances of the rewiring algorithm are explored. Results highlight the effectiveness of rewiring in containing infections to a limited number of herds for all scenarios, but especially if the outbreak is recent and if the estimation of disease prevalence is frequent. Further analysis reveal that the key parameters of the algorithm affecting infection outcome vary with the infection parameters. Allowing any animal movement from high to low-prevalence herds reduces the effectiveness of the algorithm in epidemic settings, while frequent and fine-grained prevalence assessments improve the impact of the algorithm in endemic settings. According to our results, our approach focusing on a few commercial movements is expected to lead to substantial improvements in the control of a targeted disease, although changes in the network structure should be monitored for potential vulnerabilities to other diseases. Due to its generality, the developed rewiring algorithm could be applied to any network of controlled individual movements liable to spread disease.
SARS-CoV-2 Omicron BA.2.75 variant may be much more infective than preexisting variants
Authors: Sugano Aki , Takaoka Yutaka , Kataguchi Haruyuki , Kumaoka Minoru , Ohta Mika , Kimura Shigemi , Araki Masatake , Morinaga Yoshitomo , Yamamoto Yoshihiro
Published: August 2022

Objectives

In our previous research, we developed a mathematical model via molecular simulation analysis to predict the infectivity of seven SARS-CoV-2 variants. In this report, we aimed to predict the relative risk of the recent new variants of SARS-CoV-2 as based on our previous research.

Methods

We subjected Omicron BA.4/5 and BA.2.75 variants of SARS-CoV-2 to the analysis to determine the absolute evolutionary distance of the spike protein gene (S gene) of the variants from the Wuhan variant so as to appreciate the changes in the spike protein. We performed the molecular docking simulation analyses of the spike proteins with human angiotensin-converting enzyme 2 (ACE2) to understand the docking affinities of these variants. We then compared the evolutionary distances and the docking affinities of these variants with those of the seven variants that we had analyzed in our previous research.

Results

The evolutionary distances of the S gene in BA.4/5 and BA.2.75 from the Wuhan variant were longer than those of the other variants. BA.2.75 had the highest docking affinity of the spike protein with ACE2 (ratio per Wuhan variant).

Conclusion

The important results from this analysis are the following: BA.2.75 has both the highest docking affinity and the longest evolutionary distance of the S gene. These results suggest that BA.2.75 infection can spread farther than can infections of preexisting variants.
Paradoxical tumor suppressive role of the musculoaponeurotic fibrosarcoma gene in colorectal cancer
Authors: Itakura Hiroaki , Hata Tsuyoshi , Okuzaki Daisuke , Takeda Koki , Iso Kenji , Qian Yamin , Morimoto Yoshihiro , Adachi Tomohiro , Hirose Haruka , Yokoyama Yuhki , Ogino Takayuki , Miyoshi Norikatsu , Takahashi Hidekazu , Uemura Mamoru , Mizushima Tsunekazu , Hinoi Takao , Mori Masaki , Doki Yuichiro , Eguchi Hidetoshi , Yamamoto Hirofumi
Published: August 2022

Somatic cell reprogramming using the microRNAs miR200c, miR-302s, and miR-369s leads to increased expression of cyclin-dependent kinase inhibitors in human colorectal cancer (CRC) cells and suppressed tumor growth. Here, we investigated whether these microRNAs inhibit colorectal tumorigenesis in CPC;Apc mice, which are prone to colon and rectal polyps. Repeated administration of microRNAs inhibited polyp formation. Microarray analysis indicated that c-MAF, which reportedly shows oncogene-like behavior in multiple myeloma and T-cell lymphoma, decreased in tumor samples but increased in microRNA-treated normal mucosa. Immunohistochemistry identified downregulation of c-MAF as an early tumorigenesis event in CRC, with low c-MAF expression associated with poor prognosis. Of note, c-MAF expression and p53 protein levels were inversely correlated in CRC samples. c-MAF knockout led to enhanced tumor formation in azoxymethane/dextran sodium sulfate–treated mice, with activation of cancer-promoting genes. c-MAF may play a tumor-suppressive role in CRC development.
Multimodal brain age estimates relate to Alzheimer disease biomarkers and cognition in early stages: a cross-sectional observational study
Authors: Millar Peter R , Gordon Brian A , Luckett Patrick H , Benzinger Tammie LS , Cruchaga Carlos , Fagan Anne M , Hassenstab Jason J , Perrin Richard J , Schindler Suzanne E , Allegri Ricardo F , Day Gregory S , Farlow Martin R , Mori Hiroshi , Nübling Georg ,   the Dominantly Inherited Alzheimer Network, Bateman Randall J , Morris John C , Ances Beau M
Published: August 2022

Background

Estimates of “brain-predicted age” quantify apparent brain age compared to normative trajectories of neuroimaging features. The brain age gap (BAG) between predicted and chronological age is elevated in symptomatic Alzheimer disease (AD), but has not been well explored in preclinical AD. Prior studies have typically modeled BAG with structural magnetic resonance imaging (MRI), but more recently other modalities, including functional connectivity (FC) and multimodal MRI, have been explored.

Methods

We trained three models to predict age from FC, volumetric (Vol), or multimodal MRI (Vol+FC) in 390 control participants (18-89 years old). In independent samples of 144 older adult controls, 154 preclinical AD participants, and 154 cognitively impaired (CI; CDR > 0) participants, we tested relationships between BAG and AD biomarkers of amyloid, tau, and neurodegeneration, as well as a global cognitive composite.

Results

All models predicted age in the control training set, with the multimodal model outperforming the unimodal models. All three BAG estimates were significantly elevated in CI compared to controls. FC-BAG and Vol+FC-BAG were marginally reduced in preclinical AD participants compared to controls. In CI participants only, elevated Vol-BAG and Vol+FC-BAG were associated with more advanced AD pathology and lower cognitive performance.

Conclusions

Both FC-BAG and Vol-BAG are elevated in CI participants. However, FC and volumetric MRI also capture complementary signals. Specifically, FC-BAG may capture a unique biphasic response to preclinical AD pathology, while Vol-BAG may capture pathological progression and cognitive decline in the symptomatic stage. A multimodal age-prediction model captures these modality-specific patterns, and further, improves sensitivity to healthy age differences.

Funding

This work was supported by the National Institutes of Health (P01-AG026276, P01-AG03991, P30-AG066444, 5-R01-AG052550, 5-R01-AG057680, 1-R01-AG067505, 1S10RR022984-01A1, U19-AG032438), the BrightFocus Foundation (A2022014F), and the Alzheimer’s Association (SG-20-690363-DIAN).
Cooperative host-microbe metabolism of a plant toxin in bees
Authors: Motta Erick V. S. , Gage Alejandra , Smith Thomas E. , Blake Kristin J. , Kwong Waldan K. , Riddington Ian M. , Moran Nancy A.
Published: August 2022

During pollination, bees are exposed to a myriad of xenobiotics, including plant metabolites, which may exert a wide range of effects on their health. Although bees encode enzymes that help in the metabolism of xenobiotics, they still have reduced detoxification gene diversity when compared to other insects, and may rely on other components of their physiology, such as the microbiota, to degrade potentially toxic molecules. In this study, we show that amygdalin, a cyanogenic glycoside found in honey bee-pollinated almond trees, can be metabolized by both bees and members of the gut microbiota. In microbiota-deprived bees, amygdalin is degraded into prunasin, leading to prunasin accumulation in the midgut and hindgut. In microbiota-colonized bees, on the other hand, amygdalin is degraded even further, and prunasin does not accumulate in the gut, suggesting that the microbiota contribute to the full degradation of amygdalin into hydrogen cyanide.In vitroexperiments demonstrated that amygdalin degradation by bee gut bacteria is strain-specific and not characteristic of a particular genus or species. We found strains ofBifidobacterium,BombilactobacillusandGilliamellathat can degrade amygdalin, and the degradation mechanism appears to vary since only some strains produce prunasin as an intermediate. Finally, we investigated the basis of degradation inBifidobacteriumwkB204, a strain that fully degrades amygdalin. We found overexpression and secretion of several carbohydrate-degrading enzymes, including one in glycoside hydrolase family 3 (GH3). We expressed this GH3 inEscherichia coliand detected prunasin as a byproduct when cell lysates were cultured with amygdalin, supporting its contribution to amygdalin degradation. These findings demonstrate that both host and microbiota can act together to metabolize dietary plant metabolites. How amygdalin degradation into hydrogen cyanide affects bee health remains to be elucidated.
SAMHD1 controls nucleoside-based cancer therapeutics, deoxyguanosine toxicity, and inflammation
Authors: Moore Michael D. , Johnson Errin , Jacklin Chloe , Johnson Steven , Green Owen , James William
Published: August 2022

SAMHD1 is a key regulator of dNTP metabolism, being activated by dGTP and converting dNTPs into their respective nucleosides. As a result, it plays a significant role in several distinct diseases. Not only is SAMHD1 a restriction factor for HIV-1 replication, which requires dNTPs for replication, but it is also required for genome stability, is mutated in multiple cancers, and loss of function mutations cause Acardi-Goutières Syndrome, an early-onset inherited encephalopathy. In this paper we knock out the SAMHD1 gene in pluripotent stem cells, and show that it also affects nucleoside analogue sensitivity of dividing cells and deoxyguanosine toxicity in a cell cycle-independent manner. Comparing wild type and gene-edited macrophages, we also show that deoxyguanosine toxicity is associated with pro-inflammatory cell death, modifications in uric acid production and the formation of monosodium urate crystals within the macrophages. These novel features of the SAMHD1−/− phenotype provide unique insights into the aetiology of Acardi-Goutières Syndrome, and have implications for certain chemotherapeutic agents.
TMEM100, a Lung-Specific Endothelium Gene
Authors: Liu Bin , Yi Dan , Yu Zhiyun , Pan Jiakai , Ramirez Karina , Li Shuai , Wang Ting , Glembotski Christopher C. , Fallon Michael B. , Oh S. Paul , Gu Mingxia , Kalucka Joanna , Dai Zhiyu
Published: August 2022

The heterogeneity of endothelium across different organs was recently explored using single-cell RNA-sequencing analysis. Compared to other organs, the lung exhibits a distinct structure composed of a thin layer of capillary for efficient gas exchange. In this study, we demonstrate that Tmem100 is a lung-specific endothelium gene.
Identification and characterization of repressive domains in Drosophila transcription factors
Authors: Klaus Loni , de Almeida Bernardo P. , Vlasova Anna , Nemčko Filip , Schleiffer Alexander , Bergauer Katharina , Rath Martina , Stark Alexander
Published: August 2022

All multicellular life relies on differential gene expression, determined by regulatory DNA elements and DNA-binding transcription factors that mediate activation and repression via cofactor recruitment. While activators have been extensively characterized, repressors are less well studied and their repressive domains (RDs) are typically unknown, as are the RDs’ properties and the co-repressors (CoRs) they recruit. Here, we develop the high-throughput next-generation-sequencing-based method Repressive-Domain (RD)-seq to systematically identify RDs in complex libraries. Screening more than 200,000 fragments covering the coding sequences of all transcription-related proteins in Drosophila melanogaster, we identify 195 RDs in known repressors and in proteins not previously associated with repression. Many RDs contain recurrent short peptide motifs that are required for RD function, as demonstrated by motif mutagenesis, and are conserved between fly and human. Moreover, we show that RDs which contain one of five distinct repressive motifs interact with and depend on different CoRs, including Groucho, CtBP, Sin3A or Smrter. Overall, our work constitutes an invaluable resource and advances our understanding of repressors, their sequences, and the functional impact of sequence-altering mutations.
Microcirculatory dysfunction associates with neurovascular uncoupling in peri-ischemic brain regions after ischemic stroke
Authors: Staehr Christian , Giblin John T. , Gutiérrez-Jiménez Eugenio , Guldbrandsen Halvor , Tang Jianbo , Sandow Shaun L. , Boas David A. , Matchkov Vladimir V.
Published: August 2022

Background

Despite recanalization after ischemic stroke, neurovascular coupling, i.e., the local hyperaemic response to neuronal activity, is impaired in peri-ischemic brain regions. Reduced neurovascular coupling may contribute to neurological deterioration over time. The mechanism underlying dysfunctional neurovascular coupling following stroke is largely unknown.

Methods

Mice implanted with chronic cranial windows were trained for awake head-fixation prior to experiments. One hour occlusion of the anterior middle cerebral artery branch was induced using single vessel photothrombosis. Cerebral perfusion and neurovascular coupling were assessed by optical coherence tomography and laser speckle contrast imaging. Capillaries and pericytes were studied in perfusion-fixed tissue by labelling lectin and platelet-derived growth factor receptor β.

Results

Arterial occlusion induced on average 11 spreading depressions over one hour associated with substantially reduced blood flow in the peri-ischemic cortex. Approximately half of the capillaries in the peri-ischemic area were no longer perfused 3 and 24 hours after reperfusion, which was associated with constriction of an equivalent proportion of peri-ischemic capillary pericytes. The capillaries in the peri-ischemic cortex that remained perfused showed increased prevalence of dynamic flow stalling. Whisker stimulation led to reduced neurovascular coupling responses in the sensory cortex corresponding to the peri-ischemic region 3 and 24 hours after reperfusion.

Conclusion

Arterial occlusion led to constriction of pericytes in the peri-ischemic cortex associated with long-lasting microcirculatory failure. This reduced capillary capacity may, at least in part, underlie impaired neurovascular coupling in peri-ischemic brain regions after stroke and reperfusion.
NEUROTRANSMITTER TRANSPORTER/RECEPTOR CO-EXPRESSION SHARES ORGANIZATIONAL TRAITS WITH BRAIN STRUCTURE AND FUNCTION
Authors: Hänisch Benjamin , Hansen Justine Y. , Bernhardt Boris C. , Eickhoff Simon B. , Dukart Juergen , Misic Bratislav , Valk Sofie L.
Published: August 2022

The relationship between brain areas based on neurotransmitter receptor and transporter molecule expression patterns may provide a link between brain structure and its function. Here, we studied the organization of the receptome, a measure of regional neurotransmitter receptor/transporter molecule (NTRM) similarity, derived from in vivo PET imaging studies of 19 different receptors and transporters. Nonlinear dimensionality reduction revealed three main spatial gradients of receptor similarity in the cortex. The first gradient differentiated the somato-motor network from the remaining cortex. The second gradient spanned between temporo-occipital and frontal anchors, differentiating visual and limbic networks from attention and control networks, and the third receptome gradient was anchored between the occipital and temporal cortices. In subcortical structures, the receptome delineated a striato-thalamic axis, separating functional communities. Moreover, we observed similar organizational principles underlying receptome differentiation in cortex and subcortex, indicating a link between subcortical and cortical NTRM patterning. Overall, we found that the cortical receptome shared key organizational traits with brain structure and function. Node-level correspondence of receptor similarity to functional, microstructural, and diffusion MRI-based measures decreased along a primary-to-transmodal gradient. Compared to primary and paralimbic regions, we observed higher receptomic diversification in unimodal and heteromodal regions, possibly supporting functional flexibility. In sum, we show how receptor similarity may form an additional organizational layer of human brain architecture, bridging brain structure and function.
A stress-responsive p38 signaling axis in choanoflagellates
Authors: Rutaganira Florentine U.N. , Coyle Maxwell C. , Scopton Alex P. , Dar Arvin C. , King Nicole
Published: August 2022

Animal kinases regulate cellular responses to environmental stimuli, including cell differentiation, migration, survival, and response to stress, but the ancestry of these functions is poorly understood. Choanoflagellates, the closest living relatives of animals, encode homologs of diverse animal kinases and have emerged as model organisms for reconstructing animal origins. However, efforts to study kinase signaling in choanoflagellates have been constrained by the limitations of currently available genetic tools. Here we demonstrate that small molecule approaches provide a complementary and scalable approach for studying kinase function in choanoflagellates. To study the physiological roles of choanoflagellate kinases, we established two high-throughput platforms to screen the model choanoflagellateSalpingoeca rosettawith a curated library of human kinase inhibitors. We identified 95 diverse kinase inhibitors that disruptS. rosettacell proliferation. By exploring structure-activity relationships of one inhibitor, sorafenib, we identified a p38 kinase as a regulator of heat and oxidative stress inS. rosetta. This finding indicates a conserved p38 function between choanoflagellates, animals, and fungi. Moreover, this study demonstrates that existing kinase inhibitors can serve as powerful tools to examine the ancestral roles of kinases that regulate modern animal development.
Unraveling the genetic architecture of the adaptive potential of Arabidopsis thaliana to face the bacterial pathogen Pseudomonas syringae in the context of global change
Authors: Bartoli Claudia , Rigal Mylène , Mayjonade Baptiste , Roux Fabrice
Published: August 2022

Phytopathogens are a continuous threat for global food production and security. Emergence or re-emergence of plant pathogens is highly dependent on the environmental conditions affecting pathogen spread and survival. Under climate change, a geographic expansion of pathogen distribution poleward has been observed, potentially resulting in disease outbreaks on crops and wild plants. Therefore, estimating the adaptive potential of plants to novel epidemics and describing its underlying genetic architecture, is a primary need to propose agricultural management strategies reducing pathogen outbreaks and to breed novel plant cultivars adapted to pathogens that might spread in novel habitats under climate change. To address this challenge, we inoculated Pseudomonas syringae strains isolated from Arabidopsis thaliana populations located in south-west of France on the highly genetically polymorphic TOU-A A. thaliana population located east-central France. While no adaptive potential was identified in response to most P. syringae strains, the TOU-A population displays a variable disease response to the P. syringae strain JACO-CL belonging to the phylogroup 7 (PG7). This strain carried a reduced T3SS characteristic of the PG7 as well as flexible genomic traits and potential novel effectors. GWA mapping on 192 TOU-A accessions inoculated with JACO-CL revealed a polygenic architecture. The main QTL region encompasses two R genes and the AT5G18310 gene encoding for ubiquitin hydrolase, a target of the AvrRpt2 P. syringae effector. Altogether, our results pave the way for a better understanding of the genetic and molecular basis of the adaptive potential in an ecologically relevant A. thaliana – P. syringae pathosystem.
Probabilistic tensor decomposition extracts better latent embeddings from single-cell multiomic data
Authors: Wang Ruohan , Wang Jianping , Li Shuai Cheng
Published: August 2022

Single-cell sequencing technology enables the simultaneous capture of multiomic data from multiple cells. The captured data can be represented by tensors, i.e., the higher-rank matrices. However, the proposed analysis tools often take the data as a collection of two-order matrices, renouncing the correspondences among the features. Consequently, we propose a probabilistic tensor decomposition framework, SCOIT, to extract embeddings from single-cell multiomic data. To deal with sparse, noisy, and heterogeneous single-cell data, we incorporate various distributions in SCOIT, including Gaussian, Poisson, and negative binomial distributions. Our framework can decompose a multiomic tensor into a cell embedding matrix, a gene embedding matrix, and an omic embedding matrix, allowing for various downstream analyses. We applied SCOIT to seven single-cell multiomic datasets from different sequencing protocols. With cell embeddings, SCOIT achieves superior performance for cell clustering compared to seven state-of-the-art tools under various metrics, demonstrating its ability to dissect cellular heterogeneity. With the gene embeddings, SCOIT enables cross-omics gene expression analysis and integrative gene regulatory network study. Furthermore, the embeddings allow cross-omics imputation simultaneously, outperforming conventional imputation methods with the Pearson correlation coefficient increased by 0.03-0.28.
Niacinamide enhances cathelicidin mediated SARS-CoV-2 membrane disruption
Authors: Bhatt Tanay , Khedkar Sneha Uday , Dam Binita , Lall Sahil , Pandey Subhashini , Kataria Sunny , Dias Paul M , Waskar Morris , Raut Janhavi , Sundaramurthy Varadharajan , Vemula Praveen Kumar , Ghatlia Naresh , Majumdar Amitabha , Jamora Colin
Published: August 2022

The continual emergence of new SARS-CoV-2 variants threatens the effectiveness of worldwide vaccination programs and highlights the need for complementary strategies for a sustainable containment plan. A promising approach is to mobilize the body⍰s own antimicrobial peptides (AMPs), to combat SARS-CoV-2 infection and propagation. We have found that human cathelicidin (LL37), an AMP found at epithelial barriers as well as in various bodily fluids, has the capacity to neutralise multiple strains of SARS-CoV-2. Biophysical and computational studies indicate that LL37⍰s mechanism of action is through the disruption of the viral membrane. This antiviral activity of LL37 is enhanced by the hydrotropic action of niacinamide, which may increase the bioavailability of the AMP. Interestingly, we observed inverse correlation between LL37 levels and disease severity of COVID-19 positive patients, suggesting enhancement of AMP response would be an effective therapeutic avenue to mitigate disease severity and overcome vaccine escape.
Activation of mTOR by release of extracellular cholesterol stores controls the transition from quiescence to growth in C. elegans
Authors: Schmeisser Kathrin , Kaptan Damla , Raghuraman Bharath Kumar , Shevchenko Andrej , Penkov Sider , Kurzchalia Teymuras V.
Published: August 2022

Recovery from the quiescent developmental stage called dauer is an essential process in C. elegans and provides an excellent model to understand how metabolic transitions contribute to developmental plasticity. We here show that the depletion of sterol-binding proteins SCL-12 and SCL-13 is the key change in the C. elegans proteome in early dauer recovery. This process releases a cholesterol store that is sequestered in the gut lumen during the dauer state to facilitate the transition into reproductive development. First, the stored cholesterol undergoes endocytosis into the lysosomes of the intestinal cells, where it activates mTOR to promote protein synthesis and growth. Second, it is used for the production of dafachronic acids that switch metabolic programs at the transcriptional level. These processes are essential for population fitness and survival, as loss of SCL-12 and SCL-13, depletion of sterols, and loss of mTOR precludes quiescence exit, ultimately leading to the expiration of the entire population.
Circadian Gene Expression in Mouse Renal Proximal Tubule
Authors: Bingham Molly A. , Neijman Kim , Kikuchi Hiroaki , Jung Hyun Jun , Poll Brian G. , Raghuram Viswanathan , Park Euijung , Yang Chin-Rang , Chou Chung-Lin , Chen Lihe , Leipziger Jens , Knepper Mark A. , Dona Margo
Published: August 2022

Circadian variability in kidney function has long been recognized but is often ignored as a potential confounding variable in in vivo physiological experiments. To provide a guide for physiological studies on the kidney proximal tubule, we have now created a data resource consisting of expression levels for all measurable mRNA transcripts in microdissected proximal tubule segments from mice as a function of the time of day. This approach employs small-sample RNA-sequencing (RNA-seq) applied to microdissected renal proximal tubules including both S1 proximal convoluted tubules (PCTs) and S2 proximal straight tubules (PSTs). The data were analyzed using JTK-Cycle to detect periodicity. The data are provided as a user-friendly web page at https://esbl.nhlbi.nih.gov/Databases/Circadian-Prox/. In PCTs, 234 transcripts were found to vary in a circadian manner (3.7 % of total quantified). In PSTs, 334 transcripts were found to vary in a circadian manner (5.3 % of total quantified). Transcripts previously known to be associated with corticosteroid action and transcripts associated with increased flow were found to be overrepresented among circadian transcripts peaking during the “dark” portion of the day (Zeitgeber 14-22), corresponding to the peak levels of corticosterone and glomerular filtration rate in mice.

Blurb

Circadian variation in gene expression can be an important determinant in the regulation of kidney function. The authors used RNA-seq in microdissected proximal S1 and S2 segments to identify transcripts that vary in a circadian manner. The data were used to construct a user-friendly web resource.
CNTNAP4 signaling regulates osteosarcoma disease progression
Authors: Qin Qizhi , Ramesh Sowmya , Gomez-Salazar Mario , Zhong Lingke , Cherief Masnsen , Pratapneni Aniket , Morris Carol D. , McCarthy Edward F. , Zhang Xinli , James Aaron W.
Published: August 2022

Improved treatment strategies for sarcoma rely on clarification of the molecular mediators of disease progression. Recently, we reported that the secreted glycoprotein NELL-1 modulates osteosarcoma (OS) disease progression in part via altering the sarcomatous extracellular matrix (ECM) and cell-ECM interactions. Of known NELL-1 interactor proteins, Contactin-associated protein-like 4 (Cntnap4) encodes a member of the neurexin superfamily of transmembrane molecules best known for its presynaptic functions in the central nervous system. Here, CRISPR/Cas9 gene deletion ofCNTNAP4reduced OS tumor growth, sarcoma-associated angiogenesis, and pulmonary metastases.CNTNAP4knockout (KO) in OS tumor cells largely phenocopied the effects ofNELL-1KO, including reductions in sarcoma cell attachment, migration, and invasion. Further,CNTNAP4KO cells were found to be unresponsive to the effects of NELL-1 treatment. Transcriptomic analysis combined with protein phospho-array demonstrated notable reductions in the MAPK/ERK signaling cascade withCNTNAP4deletion, and the ERK1/2 agonist isoproterenol restored cell functions amongCNTNAP4KO tumor cells. Finally, human primary cells and tissues in combination with sequencing datasets confirmed the significance ofCNTNAP4signaling in human sarcomas. In summary, our findings demonstrate the biological importance of NELL-1/CNTNAP4 signaling axis in disease progression of human sarcomas and suggest that targeting the NELL-1/CNTNAP4 signaling pathway represents a strategy with potential therapeutic benefit in sarcoma patients.
Intestinal lamina propria supports acquired eTreg suppressor function
Authors: Gu Yisu , Bartolomé-Casado Raquel , Xu Chuan , Janney Alina , Heuberger Cornelia , Pearson Claire , Teichmann Sarah , Thornton Emily E , Powrie Fiona
Published: August 2022

The intestinal immune system must maintain tolerance to commensal microbiota and self antigens whilst defending against invading pathogens. Recognising how homeostasis is established and maintained in a complex immune environment such as the gut is critical to understanding how to re-establish tolerance once broken in inflammatory disorders. Peripherally induced regulatory T cells (Tregs) play a key role in homeostasis. In intestinal tissue, Tregs work in concert with a diverse network of cells but which cellular interactions occur to instruct Treg adaptation and acquisition of distinct Treg suppressor function is not clear. We used two-photonin vivolive imaging and NICHE-seq [1] to deep phenotypeHelicobacter hepaticus(Hh)-specific Tregs with shared specificity but distinct spatially compartmentalised functions in the tissue. We show transcriptionally distinct central Treg (cTreg) and effector Treg (eTreg) populations in lymphoid versus gut tissue. The lamina propria (LP), and not embedded lymphoid aggregates (LA), is the key location of acquired immune suppressor eTreg function. Tregs recruited to the LP compartment are the dominant interacting cell type and acquired a more effector Treg profile with upregulation ofAreg, Gzmb, Icos, Tigit, Tnfrsf4(OX40), andTnfrsf18(GITR). We identify IL-1β+macrophages, CD206+ macrophages, and ILC2 in the LP niche as the key players governing Treg survival and function. In contrast, LA, dominated by interactions with ILC3s and populations of IL-6+DCs, are equipped to tip the balance towards a pro-inflammatory response. By functionally isolating the gut tissue from secondary lymphoid organs, we show that eTregs maintain their phenotype in the context of inflammatory insult. Blocking their key effector molecule, IL-10, results in locally differentiated Th17 cell proliferation without overt inflammation due to local IL-10 independent mechanisms that constrain inflammation. Our results reveal a previously unrecognised spatial mechanism of tolerance, and demonstrate how knowledge of local interactions can guide cell function and potentially be manipulated for the next generation of tolerance-inducing therapies.
The differential effect of age on upper limb sensory processing, proprioception and motor function
Authors: Saenen Leen , Verheyden Geert , Orban de Xivry Jean-Jacques
Published: August 2022

Sensory processing consists in the integration and interpretation of somatosensory information. It builds upon proprioception but is a distinct function requiring complex processing by the brain over time. Currently little is known about the effect of aging on sensory processing ability, nor the influence of other covariates such as motor function, proprioception, or cognition. In this study, we measured upper limb passive and active sensory processing, motor function, proprioception, and cognition in 40 healthy younger adults and 54 older adults. We analyzed age differences across all measures and evaluated the influence of covariates on sensory processing through regression. Our results showed larger effect sizes for age differences in sensory processing (r=0.38) compared to motor function (r=0.18-0.22) and proprioception (r=0.10-0.27), but smaller than for cognition (r=0.56-0.63). Aside from age, we found no evidence that sensory processing performance was related to motor function or proprioception, but active sensory processing was related to cognition (β=0.30-0.42). In conclusion, sensory processing showed an age-related decline, while some proprioceptive and motor abilities were preserved across age.
Probabilistic axon targeting dynamics lead to individualized brain wiring
Authors: Andriatsilavo Maheva , Dumoulin Alexandre , Dutta Suchetana Bias , Stoeckli Esther T. , Hiesinger P. Robin , Hassan Bassem A.
Published: August 2022

Developmental variation in brain-wiring contributes to behavioural individuality1,2. However, how and when individualized wiring diagrams emerge and become stable during development remains largely unknown. Here, we explored axon targeting dynamics in individual brains using live-imaging of a developing Drosophila visual circuit and discovered that targeting choice is an algorithmic multi-step growth process with variable outcomes. Using optogenetics, we found that temporally restricted Notch lateral-inhibition defines a subset of neurons with a probabilistic potential to innervate distal targets. Next, axons from NotchOFF neurons amplify into long actin-rich multi-fibre structures necessary for distal growth. A subset of these NotchOFF neurons create distal targeting axons by stabilizing microtubule growth in one of their actin fibres. Amplified axons without tubulin-stabilized fibres retract, resulting in the stochastic selection of a different number of distal targeting axons in each brain. Pharmacological microtubule destabilization suffices to inhibit this targeting. We observed a similar axonal amplification-stabilization process in the developing chick spinal cord, suggesting a conserved mechanism. Finally, early microtubule patterns predict the adult brain-wiring of an individual in a target-independent manner prior to synapse formation3,4. Thus, we show that a temporal succession of genetically encoded stochastic processes explains the emergence of individual wiring variation.

One-Sentence Summary

The temporal succession of stochastic developmental processes explains the emergence of individual wiring variation.
Relating enhancer genetic variation across mammals to complex phenotypes using machine learning
Authors: Kaplow Irene M. , Lawler Alyssa J. , Schäffer Daniel E. , Srinivasan Chaitanya , Wirthlin Morgan E. , Phan BaDoi N. , Zhang Xiaomeng , Foley Kathleen , Prasad Kavya , Brown Ashley R. ,   Zoonomia Consortium, Meyer Wynn K. , Pfenning Andreas R.
Published: August 2022

Protein-coding differences between mammals often fail to explain phenotypic diversity, suggesting involvement of enhancers, often rapidly evolving regions that regulate gene expression. Identifying associations between enhancers and phenotypes is challenging because enhancer activity is context-dependent and may be conserved without much sequence conservation. We developed TACIT (Tissue-Aware Conservation Inference Toolkit) to associate open chromatin regions (OCRs) with phenotypes using predictions in hundreds of mammalian genomes from machine learning models trained to learn tissue-specific regulatory codes. Applying TACIT for motor cortex and parvalbumin-positive interneurons to neurological phenotypes revealed dozens of new OCR-phenotype associations. Many associated OCRs were near relevant genes, including brain size-associated OCRs near genes mutated in microcephaly or macrocephaly. Our work creates a forward genomics foundation for identifying candidate enhancers associated with phenotype evolution.

One Sentence Summary

A new machine learning-based approach associates enhancers with the evolution of brain size and behavior across mammals.
Challenges in Improving Genomic Literacy: Results from National and Regional Surveys of Genomic Knowledge, Attitudes, Concerns, and Behaviors
Authors: Jaeger Joseph , Hellwig Amanda , Schiavoni Elizabeth , Brace-MacDonald Bridget , Lamb Natalie A. , Tumiel-Berhalter Laurene , Halfon Marc S. , Vishwanath Arun , Surtees Jennifer A.
Published: August 2022

Purpose

Information about genomics is increasingly available to mainstream society, with more and more emphasis on using genomic information to make health care decisions. To determine how prepared people are to use this knowledge to make critical health-related decisions, we assessed the public’s level of genomic literacy and whether this knowledge affects their engagement in behaviors related to genomics, such as getting genetic testing.

Methods

A survey assessing perceived and actual knowledge, attitudes, concerns, sources of information, and behaviors related to genomics was administered to national and regional samples of participants. A hierarchical linear regression tested whether knowledge and attitudes predicted engagement in behaviors related to genomics.

Results

Participants had good basic knowledge of genetics, though they were less familiar with the term “the human genome.” They also displayed positive attitudes towards genomic research, despite expressing many concerns. Both greater knowledge and more positive attitudes significantly and independently predicted greater engagement in genetic testing and other related proactive health behaviors.

Conclusion

Knowledge and concerns about genomics impact the public’s ability and willingness to obtain genetic testing and engage in other proactive health behaviors. The public’s genomic literacy could be enhanced by integrating their knowledge (e.g of DNA) with broader concepts (e.g. the human genome and genomics) and how they relate to health. Future research is needed on interventions that do this, to improve the public’s genomic literacy through relationships that build trust
DEEP LEARNING ENABLED MULTI-ORGAN SEGMENTATION OF MOUSE EMBRYOS
Authors: Rolfe S.M. , Maga A. M.
Published: August 2022

The International Mouse Phenotyping Consortium (IMPC) has generated a large repository of 3D imaging data from mouse embryos, providing a rich resource for investigating phenotype/genotype interactions. While the data is freely available, the computing resources and human effort required to segment these images for analysis of individual structures can create a significant hurdle for research. In this paper, we present an open source, deep learning-enabled tool, Mouse Embryo Multi-Organ Segmentation (MEMOS), that estimates a segmentation of 50 anatomical structures with a support for manually reviewing, editing, and analyzing the estimated segmentation in a single application. MEMOS is implemented as an extension on the 3D Slicer platform and is designed to be accessible to researchers without coding experience. We validate the performance of MEMOS-generated segmentations through comparison to state-of-the-art atlas-based segmentation and quantification of previously reported anatomical abnormalities in a CBX4 knockout strain.

SUMMARY STATEMENT

We present a new open source, deep learning-enabled tool, Mouse Embryo Multi-Organ Segmentation (MEMOS), to estimate the segmentation of 50 anatomical structures from microCT scans of embryonic mice.
Characterization of SARS-CoV-2 Omicron BA.2.75 clinical isolates
Authors: Uraki Ryuta , Iida Shun , Halfmann Peter J. , Yamayoshi Seiya , Hirata Yuichiro , Iwatsuki-Horimoto Kiyoko , Kiso Maki , Ito Mutsumi , Furusawa Yuri , Ueki Hiroshi , Sakai-Tagawa Yuko , Kuroda Makoto , Maemura Tadashi , Kim Taksoo , Mine Sohtaro , Iwamoto Noriko , Li Rong , Liu Yanan , Larson Deanna , Fukushi Shuetsu , Watanabe Shinji , Maeda Ken , Wang Zhongde , Ohmagari Norio , Theiler James , Fischer Will , Korber Bette , Imai Masaki , Suzuki Tadaki , Kawaoka Yoshihiro
Published: August 2022

The prevalence of the Omicron subvariant BA.2.75 is rapidly increasing in India and Nepal. In addition, BA.2.75 has been detected in at least 34 other countries and is spreading globally. However, the virological features of BA.2.75 are largely unknown. Here, we evaluated the replicative ability and pathogenicity of BA.2.75 clinical isolates in Syrian hamsters. Although we found no substantial differences in weight change among hamsters infected with BA.2, BA.5, or BA.2.75, the replicative ability of BA.2.75 in the lungs was higher than that of BA.2 and BA.5. Of note, BA.2.75 caused focal viral pneumonia in hamsters, characterized by patchy inflammation interspersed in alveolar regions, which was not observed in BA.5-infected hamsters. Moreover, in competition assays, BA.2.75 replicated better than BA.5 in the lungs of hamsters. These results suggest that BA.2.75 can cause more severe respiratory disease than BA.5 and BA.2 and should be closely monitored.
A polarized nuclear position is required for correct division plane specification during maize stomatal development
Authors: Ashraf M. Arif , Liu Le , Facette Michelle R.
Published: August 2022

Asymmetric cell division generates new cell types and is a feature of development in multicellular organisms. Prior to asymmetric cell division, cell polarity is established.Zea maysstomatal development serves as an excellent plant model system for asymmetric cell division, especially the asymmetric division of the subsidiary mother cell (SMC). In SMCs, the nucleus migrates to a polar location after the accumulation of polarly localized proteins, but before the appearance of the preprophase band. We examined a mutant of the outer nuclear membrane protein, which is part of the LINC (linker of nucleoskeleton and cytoskeleton) complex that localizes to the nuclear envelope in interphase cells. Previously,mlks2(maize linc kash sine-like2) was observed to have abnormal stomata. We confirmed and identified the precise defects that lead to abnormal asymmetric divisions. Proteins that are polarly localized in SMCs prior to division polarize normally inmlks2. However, polar localization of the nucleus is sometimes impaired, even in cells that have otherwise normal polarity. This leads to a misplaced preprophase band and atypical division planes. MLKS2 is localized to mitotic structures, however the structure of the preprophase band, spindle and phragmoplast appeared normal inmlks2. Timelapse imaging revealed thatmlks2has defects in pre-mitotic nuclear migration towards the polarized site, and unstable position at the division site after formation of the preprophase band. We show that nuclear envelope proteins promote pre-mitotic nuclear migration and stable nuclear position, and that the position of the nucleus influences division plane establishment in asymmetrically dividing cells.

One-sentence summary

Nuclear movement and positioning prior to asymmetric cell division is required for deciding the future division site.