bluuebunny/crossref_metadata_2025 huggingface dataset:
Adversarial and variational autoencoders improve metagenomic binning
Authors: Piera Lindez Pau , Johansen Joachim , Sigurdsson Arnror Ingi , Nissen Jakob Nybo , Rasmussen Simon
Published: February 2023

Assembly of reads from metagenomic samples is a hard problem, often resulting in highly fragmented genome assemblies. Metagenomic binning allows us to reconstruct genomes by re-grouping the sequences by their organism of origin, thus representing a crucial processing step when exploring the biological diversity of metagenomic samples. Here we present Adversarial Autoencoders for Metagenomics Binning (AAMB), an ensemble deep learning approach that integrates sequence co-abundances and tetranucleotide frequencies into a common denoised space that enables precise clustering of sequences into microbial genomes. When benchmarked, AAMB presented similar or better results compared with the state-of-the-art reference-free binner VAMB, reconstructing ~7% more near-complete (NC) genomes across simulated and real data. In addition, genomes reconstructed using AAMB had higher completeness and greater taxonomic diversity compared with VAMB. Finally, we implemented a pipeline integrating VAMB and AAMB that enabled improved binning, recovering 20% and 29% more simulated and real NC genomes, respectively, compared to VAMB with moderate additional runtime. AAMB is freely available at https://github.com/RasmussenLab/VAMB.
The functional specificity of CDC42 isoforms is caused by their distinct subcellular localization
Authors: Ravichandran Yamini , Hänisch Jan , Murray Kerren , Roca Vanessa , Dingli Florent , Loew Damarys , Sabatet Valentin , Boëda Batiste , Stradal Theresia , Etienne-Manneville Sandrine
Published: February 2023

The small G-protein CDC42 is an evolutionary conserved polarity protein and a key regulator of numerous polarized cell functions, including directed cell migration. In vertebrates, alternative splicing gives rise to two CDC42 proteins: the ubiquitously expressed isoform (CDC42u) and the brain isoform (CDC42b), whose specific roles are not fully elucidated. The two isoforms only differ in their carboxy-terminal sequence, which includes the CAAX motif essential for CDC42 interaction with membrane. Here we show that these divergent sequences do not directly affect the range of CDC42’s potential binding partners, but indirectly influence CDC42-driven signaling by controlling the specific subcellular localization of the two isoforms. In astrocytes and neural precursors, which naturally express both variants, CDC42u is mainly cytosolic and associates with the leading-edge plasma membrane of migrating cells where it recruits the Par6-PKCζ complex to fulfill its polarity function. In contrast, CDC42b mainly localizes to intracellular membrane compartments, where it interacts with N-WASP. CDC42b does not participate in cell polarization but embodies the major isoform regulating endocytosis. Both CDC42 isoforms act in concert by contributing their specific functions to promote chemotaxis of neural precursors, demonstrating that the expression pattern of the two isoforms is decisive for the tissue-specific behavior of cells.
Uncovering the essential roles of human GCP 2 orthologs inCaenorhabditis elegans
Authors: Panska Lucie , Nedvedova Stepanka , Vacek Vojtech , Krivska Daniela , Konecny Lukas , Knop Filip , Kutil Zsofia , Skultetyova Lubica , Leontovyc Adrian , Ulrychova Lenka , Sakanari Judy , Asahina Masako , Barinka Cyril , Macurkova Marie , Dvorak Jan
Published: February 2023

Human glutamate carboxypeptidase 2 (GCP2) from the M28B metalloprotease group is an important target for therapy in neurological disorders and an established tumor marker. However, its physiological functions remain unclear. To better understand general roles, we used the model organismCaenorhabditis elegansgenetically manipulate its three existing orthologous genes and evaluate the impact on worm physiology. The results of gene knockout studies showed thatC. elegansGCP2 orthologs affect the pharyngeal physiology, reproduction, and structural integrity of the organism. Promoter-driven GFP expression revealed distinct localization for each of the three gene paralogs, withgcp-2.1being most abundant in muscles, intestine, and pharyngeal interneurons,gcp-2.2restricted to the phasmid neurons, andgcp-2.3located in the excretory cell. This study provides new insight into the unique phenotypic effects of GCP2 gene knockouts inC. elegans, and the specific tissue localizations. We believe that elucidation of particular roles in a non-mammalian organism can help to explain important questions linked to human GCP2 physiology and in extension to GCP2 involvement in pathophysiological processes.
Cautionary note on ribonuclease activity of recombinant PR-10 proteins
Authors: Longsaward Rawit , Sanguankiattichai Nattapong , Viboonjun Unchera , van der Hoorn Renier A.L.
Published: February 2023

We studied the biochemical properties of three splicing isoforms of PR-10 from rubber tree (Hevea brasiliensis) and found that purified recombinantHbPR10 can cause RNA degradationin vitro, a well-known activity described for many PR-10 proteins. This ribonuclease activity was observed for all threeHbPR10 splicing isoforms and is abolished by boiling. However, inclusion of a negative control proteins revealed that ribonuclease activity rather originates from RNases that are copurified fromE. coli, which are overlooked by traditionally used controls such as heat inactivation, RNase inhibitors and negative control proteins obtained with different procedures. The crucial control proteins are missing for at least nine reports on ribonuclease activity in PR-10 proteins published by different laboratories worldwide, indicating that proper controls are frequently overlooked in ribonuclease assays. The raised cautionary note applies to several PR-10 proteins with proclaimed ribonuclease activities and call for the use of different assays and mutant PR-10 proteins as control.
Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits
Authors: Beard Diana C. , Zhang Xiyun , Wu Dennis Y. , Martin Jenna R. , Hamagami Nicole , Swift Raylynn G. , McCullough Katherine B. , Ge Xia , Bell-Hensley Austin , Zheng Hongjun , Lawrence Austin B. , Hill Cheryl A. , Papouin Thomas , McAlinden Audrey , Garbow Joel R. , Dougherty Joseph D. , Maloney Susan E. , Gabel Harrison W.
Published: February 2023

Phenotypic heterogeneity is a common feature of monogenic neurodevelopmental disorders that can arise from differential severity of missense variants underlying disease, but how distinct alleles impact molecular mechanisms to drive variable disease presentation is not well understood. Here, we investigate missense mutations in the DNA methyltransferase DNMT3A associated with variable overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity in neurodevelopmental disease. We generate a DNMT3A P900L/+ mouse model mimicking a disease mutation with mild-to-moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. We show that the P900L mutation leads to disease-relevant overgrowth, obesity, and social deficits shared across DNMT3A disorder models, while the R878H mutation causes more extensive epigenomic disruption leading to differential dysregulation of enhancers elements. We identify distinct gene sets disrupted in each mutant which may contribute to mild or severe disease, and detect shared transcriptomic disruption that likely drives common phenotypes across affected individuals. Finally, we demonstrate that core gene dysregulation detected in DNMT3A mutant mice overlaps effects in other developmental disorder models, highlighting the importance of DNMT3A-deposited methylation in neurodevelopment. Together, these findings define central drivers of DNMT3A disorders and illustrate how variable disruption of transcriptional mechanisms can drive the spectrum of phenotypes in neurodevelopmental disease.
Aging seeds of weedy broomrapes and witchweeds lose sensitivity to strigolactones as DNA demethylates
Authors: Brun Guillaume , Pöhl Jonathan , Wicke Susann
Published: February 2023

Broomrapes (PhelipancheandOrobanchespp.) and witchweeds (StrigaandAlectraspp.) are obligate root parasitic weeds responsible for major crop yield losses worldwide. Their success in agricultural landscapes is attributable to their ability to produce thousands of long-lived minute seeds that coordinate their germination with the presence of nearby hosts by perceiving host-derived strigolactones. Nevertheless, the processes underlying the alleged decade(s)-long persistence in the field are understudied. Using an accelerated seed aging method coupled to germination and ELISA bioassays, we report that the loss of seed viability and germinability along seed aging is accompanied by a decrease in both strigolactone sensitivity and global DNA methylation. Our results also suggest that seeds of broomrapes are longer-lived than those of witchweeds. Overall, this study deems to initiate further research into how epigenetic mechanisms contribute to alterations in seed viability in parasitic weeds, and how seed aging influence seed responses to their environment.
SIRT6 activation rescues the age-related decline in DNA damage repair in primary human chondrocytes
Authors: Copp Michaela E. , Shine Jacqueline , Brown Hannon L. , Nimmala Kirti R. , Chubinskaya Susan , Collins John A. , Loeser Richard F. , Diekman Brian O.
Published: February 2023

While advanced age has long been recognized as the greatest risk factor for osteoarthritis (OA), the biological mechanisms behind this connection remain unclear. Previous work has demonstrated that chondrocytes from older cadaveric donors have elevated levels of DNA damage as compared to chondrocytes from younger donors. The purpose of this study was to determine whether a decline in DNA repair efficiency is one explanation for the accumulation of DNA damage with age, and to quantify the improvement in repair with activation of Sirtuin 6 (SIRT6). Using an acute irradiation model to bring the baseline level of all donors to the same starting point, this study demonstrates a decline in repair efficiency during aging when comparing chondrocytes from young (≤45 years old), middle-aged (50-65 years old), or older (>70 years old) cadaveric donors with no known history of OA or macroscopic cartilage degradation at isolation. Activation of SIRT6 in middle-aged chondrocytes with MDL-800 (20 μM) improved the repair efficiency, while inhibition with EX-527 (10 μM) inhibited the rate of repair and the increased the percentage of cells that retained high levels of damage. Treating chondrocytes from older donors with MDL-800 for 48 hours significantly reduced the amount of DNA damage, despite this damage having accumulated over decades. Lastly, chondrocytes isolated from the proximal femurs of mice between 4 months and 22 months of age revealed both an increase in DNA damage with aging, and a decrease in DNA damage following MDL-800 treatment.
In vitroreconstitution of chromatin domains
Authors: Quililan Kimberly , Oberbeckmann Elisa , Cramer Patrick , Oudelaar A. Marieke
Published: February 2023

The spatial organization of the genome modulates nuclear processes, including transcription, replication, and DNA repair1,2. Eukaryotic genomes are organized into distinct 3D chromatin domains3. However, the molecular mechanisms that drive the formation of these domains are difficult to dissectin vivoand remain poorly understood. Here, we reconstituteS. cerevisiaechromatinin vitroand determine its 3D organization at sub-nucleosome resolution by MNase-based chromosome conformation capture and molecular dynamics simulations. We show that regularly spaced and phased nucleosome arrays form chromatin domainsin vitrothat resemble domainsin vivo. This demonstrates that neither loop extrusion nor transcription are required for domain formation. In addition, we find that the boundaries of reconstituted domains correspond to nucleosome-free regions and that insulation strength scales with their width. Finally, we show that domain compaction depends on nucleosome linker length, with longer linkers forming more compact structures. Together, our results demonstrate that nucleosome positioning is sufficient to reconstitute chromatin domains and provide a proof-of-principle for bottom-up 3D genome studies.
Requirements for establishment and epigenetic stability of mammalian heterochromatin
Authors: Tatarakis Antonis , Saini Harleen , Moazed Danesh
Published: February 2023

Heterochromatic domains of DNA account for a large fraction of mammalian genomes and play critical roles in silencing transposons and genes, but the mechanisms that establish and maintain these domains are not fully understood. Here we use an inducible heterochromatin formation system combined with a CRISPR-based genetic screen to investigate the requirements for the establishment and maintenance of heterochromatin in mouse embryonic stem cells (mESCs). We show that DNA sequence-independent and histone H3 lysine 9 methylation (H3K9me)-dependent heterochromatin can be inherited for a limited number of cell divisions in mESCs but becomes stable upon differentiation. We provide evidence that the increased stability of heterochromatin in differentiated cells results from the downregulation of one or more enzymes that erase H3K9me and DNA methylation. Moreover, we show that in addition to components of the H3K9 and DNA methylation pathways, heterochromatin maintenance requires DHX9 and other RNA processing proteins. DHX9 is an RNA/DNA helicase with previously described roles in preventing genomic instability resulting from transcription-associated replication stress. We found that deletion of DHX9 results in defective heterochromatin inheritance and is associated with increased transcription of major satellite repeats, accumulation of R-loops, and loss of H3K9me. Our findings define the requirements for the establishment and epigenetic inheritance of mammalian heterochromatin and suggest that R-loops and replication stress lead to epigenetic instability.
Detecting the effect of genetic diversity on brain composition in an Alzheimer’s disease mouse model
Authors: Gurdon Brianna , Yates Sharon C. , Csucs Gergely , Groeneboom Nicolaas E. , Hadad Niran , Telpoukhovskaia Maria , Ouellette Andrew , Ouellette Tionna , O’Connell Kristen , Singh Surjeet , Murdy Tom , Merchant Erin , Bjerke Ingvild , Kleven Heidi , Schlegel Ulrike , Leergaard Trygve B. , Puchades Maja A. , Bjaalie Jan G. , Kaczorowski Catherine C.
Published: February 2023

Alzheimer’s disease (AD) is characterized by neurodegeneration, pathology accumulation, and progressive cognitive decline. There is significant variation in age at onset and severity of symptoms highlighting the importance of genetic diversity in the study of AD. To address this, we analyzed cell and pathology composition of 6- and 14-month-old AD-BXD mouse brains using the semi-automated workflow (QUINT); which we expanded to allow for nonlinear refinement of brain atlas-registration, and quality control assessment of atlas-registration and brain section integrity. Near global age-related increases in microglia, astrocyte, and amyloid-beta accumulation were measured, while regional variation in neuron load existed among strains. Furthermore, hippocampal immunohistochemistry analyses were combined with bulk RNA- sequencing results to demonstrate the relationship between cell composition and gene expression. Overall, the additional functionality of the QUINT workflow delivers a highly effective method for registering and quantifying cell and pathology changes in diverse disease models.
Sterically enhanced control of enzyme-assisted DNA assembly
Authors: Irving Oliver J , Matthews Lauren , Coulthard Steven , Neely Robert K , Grant Mellissa M. , Albrecht Tim
Published: February 2023

Traditional methods for the assembly of functionalised DNA structures, involving enzyme restriction and modification, present difficulties when working with small DNA fragments (<100bp), in part due to a lack of control over enzymatic action during the DNA modification process. This limits the design flexibility and range of accessible DNA structures. Here, we show that these limitations can be overcome by introducing chemical modifications into the DNA, which spatially restrict enzymatic activity. This approach, Sterically Controlled Nuclease Enhanced (SCoNE) DNA assembly, thereby circumvents the size limitations of conventional Gibson assembly (GA) and allows for the preparation of well-defined, functionalised DNA structures with multiple probes for specific analytes, such as IL-6, procalcitonin (PCT), and a biotin reporter group. Notably, using the same starting materials conventional GA under typical conditions fails. We demonstrate successful analyte capture based on standard and modified sandwich ELISA and also show how the inclusion of biotin probes provides additional functionality for product isolation.
Structural influences on synaptic plasticity: the role of presynaptic connectivity in the emergence of E/I co-tuning
Authors: Giannakakis Emmanouil , Vinogradov Oleg , Buendía Victor , Levina Anna
Published: February 2023

Cortical neurons are versatile and efficient coding units that develop strong preferences for specific stimulus characteristics. The sharpness of tuning and coding efficiency is hypothesized to be controlled by delicately balanced excitation and inhibition. These observations suggest a need for detailed co-tuning of excitatory and inhibitory populations. Theoretical studies have demonstrated that a combination of plasticity rules can lead to the emergence of excitation/inhibition (E/I) cotuning in neurons driven by independent, low-noise signals. However, cortical signals are typically noisy and originate from highly recurrent networks, generating correlations in the inputs. This raises questions about the ability of plasticity mechanisms to self-organize co-tuned connectivity in neurons receiving noisy, correlated inputs. Here, we study the emergence of input selectivity and weight co-tuning in a neuron receiving input from a recurrent network via plastic feedforward connections. We demonstrate that while strong noise levels destroy the emergence of co-tuning in the readout neuron, introducing specific structures in the non-plastic pre-synaptic connectivity can re-establish it by generating a favourable correlation structure in the population activity. We further show that structured recurrent connectivity can impact the statistics in fully plastic recurrent networks, driving the formation of co-tuning in neurons that do not receive direct input from other areas. Our findings indicate that the network dynamics created by simple, biologically plausible structural connectivity patterns can enhance the ability of synaptic plasticity to learn input-output relationships in higher brain areas.
RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life
Authors: Meyer McCauley O. , Yamagami Ryota , Choi Saehyun , Keating Christine D. , Bevilacqua Philip C.
Published: February 2023

Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology and has been proposed as a prebiotically-plausible way to accumulate RNA. However, compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Herein, we detail Next-Generation Sequencing (NGS) experiments performed for the first time in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Strikingly, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that covalent RNA modifications could have played a critical role in metabolic processes at the origin of life.

One Sentence Summary

We demonstrate that RNA folds into native secondary and tertiary structures in protocell models and that this is favored by covalent modifications, which is critical for the origins of life.
Notochord and axial progenitor generation by timely BMP and NODAL inhibition during vertebrate trunk formation
Authors: Rito Tiago , Libby Ashley R.G. , Demuth Madeleine , Briscoe James
Published: February 2023

The formation of the vertebrate body involves the coordinated and progressive production of trunk tissues from progenitors located in the posterior of the embryo. In vitro models based on pluripotent stem cells (PSCs) replicate aspects of this process, but they lack some tissue components normally present in the trunk. Most strikingly, the notochord, a hallmark of chordates and the source of midline signals that pattern surrounding tissues, is absent from current models of human trunk formation. To investigate how trunk tissue is formed, we performed single-cell transcriptomic analysis of chick embryos. This delineated molecularly discrete progenitor populations, which we spatially locate in the embryo, compare across species, and relate to signalling activity. Guided by this map, we determined how differentiating human PSCs develop a stereotypical spatial organization of tissue types. We found that LATS1/2 repression of YAP activity, in conjunction with FGF-mediated MAPK activation, induced the transcription factor Bra/TBXT and facilitated WNT signaling. In addition, inhibiting a WNT-induced NODAL and BMP signaling cascade at the appropriate time regulated the proportions of different tissue types produced, including notochordal cells. We used this information to create an integrated 3D model of human gastrulation undergoing morphogenetic movements to produce elongated structures with a notochord and spatially patterned neural tissue formation. Together the data provide insight into the mechanisms responsible for the formation of the tissues that comprise the vertebrate trunk and pave the way for future studies of patterning in a tissue-like environment.
Identification of pharmacological inducers of a reversible hypometabolic state for whole organ preservation
Authors: Sperry Megan M. , Charrez Berenice , Fotowat Haleh , Gardner Erica , Pilobello Kanoelani , Izadifar Zohreh , Lin Tiffany , Kuelker Abigail , Kaki Sahith , Lewandowski Michael , Lightbown Shanda , Martinez Ramses , Marquez Susan , Moore Joel , Plaza-Oliver Maria , Sesay Adama M. , Shcherbina Kostyantyn , Sheehan Katherine , Takeda Takako , Del Campo Daniela , Andrijauskaite Kristina , Cisneros Exal , Lopez Riley , Cano Isabella , Maxwell Zachary , Jessop Israel , Veraza Rafael J. , Bunegin Leon , Percival Thomas J. , Yracheta Jaclyn , Pena Jorge , Wood Diandra , Homas Zachary , Hinshaw Cody , Cox-Hinshaw Jennifer , Parry Olivia G. , Sleeter Justin J. , Weitzel Erik K. , Levin Michael , Super Michael , Novak Richard , Ingber Donald E.
Published: February 2023

Drugs that induce reversible slowing of metabolic and physiological processes would have great value for organ preservation, especially for organs with high susceptibility to hypoxia-reperfusion injury, such as the heart. Using whole-organism screening of metabolism, mobility, and development inXenopus, we identified an existing drug, SNC80, that rapidly and reversibly slows biochemical and metabolic activities while preserving cell and tissue viability. Although SNC80 was developed as a delta opioid receptor activator, we discovered that its ability to slow metabolism is independent of its opioid modulating activity as a novel SNC80 analog (WB3) with almost 1,000 times less delta opioid receptor binding activity is equally active. Metabolic suppression was also achieved using SNC80 in microfluidic human organs-on-chips, as well as in explanted whole porcine hearts and limbs, demonstrating the cross-species relevance of this approach and potential clinical relevance for surgical transplantation. Pharmacological induction of physiological slowing in combination with organ perfusion transport systems may offer a new therapeutic approach for tissue and organ preservation for transplantation, trauma management, and enhancing patient survival in remote and low-resource locations.
A molecularly defined NAcSh D1 subtype controls feeding and energy homeostasis
Authors: Liu Yiqiong , Wang Ying , Zhao Zheng-dong , Xie Guoguang , Zhang Chao , Chen Renchao , Zhang Yi
Published: February 2023

Orchestrating complex behavioral states, such as approach and consumption of food, is critical for survival. In addition to hypothalamus neuronal circuits, the nucleus accumbens (NAc) also plays an important role in controlling appetite and satiety in responses to changing external stimuli. However, the specific neuronal subtypes of NAc involved as well as how the humoral and neuronal signals coordinate to regulate feeding remain incompletely understood. Here, we deciphered the spatial diversity of neuron subtypes of the NAc shell (NAcSh) and defined a dopamine receptor D1(Drd1)- andSerpinb2-expressing subtype located in NAcSh encoding food consumption. Chemogenetics- and optogenetics-mediated regulation ofSerpinb2+neurons bidirectionally regulates food seeking and consumption specifically. Circuitry stimulation revealed the NAcShSerpinb2→LHLepRprojection controls refeeding and can overcome leptin-mediated feeding suppression. Furthermore, NAcShSerpinb2+neuron ablation reduces food intake and upregulates energy expenditure resulting in body weight loss. Together, our study reveals a neural circuit consisted of molecularly distinct neuronal subtype that bidirectionally regulates energy homeostasis, which can serve as a potential therapeutic target for eating disorders.
Engineered Immunogens to Elicit Antibodies Against Conserved Coronavirus Epitopes
Authors: Kapingidza Brenda , Marston Daniel J. , Harris Caitlin , Wrapp Daniel , Winters Kaitlyn , Mielke Dieter , Xiaozhi Lu , Yin Qi , Foulger Andrew , Parks Rob , Barr Maggie , Newman Amanda , Schäfer Alexandra , Eaton Amanda , Flores Justine Mae , Harner Austin , Cantazaro Nicholas J , Mallory Michael L , Mattocks Melissa D , Beverly Christopher , Rhodes Brianna , Mansouri Katayoun , Itallie Elizabeth Van , Vure Pranay , Manness Brooke , Keyes Taylor , Stanfield-Oakley Sherry , Woods Christopher W. , Petzold Elizabeth A. , Walter Emmanuel B , Wiehe Kevin , Edwards Robert J. , Montefiori David , Ferrari Guido , Baric Ralph , Cain Derek W. , Saunders Kevin O. , Haynes Barton F. , Azoitei Mihai L.
Published: February 2023

Immune responses to SARS-CoV-2 primarily target the receptor binding domain of the spike protein, which continually mutates to escape acquired immunity. Other regions in the spike S2 subunit, such as the stem helix and the segment encompassing residues 815-823 adjacent to the fusion peptide, are highly conserved across sarbecoviruses and are recognized by broadly reactive antibodies, providing hope that vaccines targeting these epitopes could offer protection against both current and emergent viruses. Here we employed computational modeling to design scaffolded immunogens that display the spike 815-823 peptide and the stem helix epitopes without the distracting and immunodominant RBD. These engineered proteins bound with high affinity and specificity to the mature and germline versions of previously identified broadly protective human antibodies. Epitope scaffolds interacted with both sera and isolated monoclonal antibodies with broadly reactivity from individuals with pre-existing SARS-CoV-2 immunity. When used as immunogens, epitope scaffolds elicited sera with broad betacoronavirus reactivity and protected as “boosts” against live virus challenge in mice, illustrating their potential as components of a future pancoronavirus vaccine.
Characterization of early white matter changes in CADASIL using microscopic diffusion imaging and relaxometry
Authors: Barrière David A. , Uszynski Ivy , Rajani Rikesh M. , Gueniot Florian , Domenga-Denier Valérie , Boumezbeur Fawzi , Poupon Cyril , Joutel Anne
Published: February 2023

Background and purpose

Cerebral small vessel diseases (SVDs) are characterized by early white matter (WM) changes, whose pathological underpinnings are yet poorly understood. CADASIL is a monogenic and archetypal SVD, providing an ideal model for investigating these changes. Here, we used multicompartment microscopic diffusion imaging and relaxometry to elucidate microstructural changes underlying early WM abnormalities in CADASIL.

Methods

We acquired diffusion MRI data with a multiple-shell Q-space sampling strategy, and relaxometry T1 and T2 data, with a 160 and 80-μm isotropic resolution respectively,ex vivo, in CADASIL and control mice. Diffusion datasets were computed with the Neurite Orientation Dispersion and Density Imaging model to extract the neurite density index, the extracellular free water and the orientation dispersion index. Relaxometry datasets were computed with a 3-compartment myelin water imaging model to extract the myelin content. MRI metrics were compared between CADASIL and control mice using voxel and WM tract-based analyses and with electron microscopy analysis.

Results

WM in CADASIL mice displayed a widespread reduction in general fractional anisotropy, a large increase in extracellular free water, a reduction in the myelin content, but no reduction in neurite density. Electron microscopy analysis showed a ∽2-fold increase in the extracellular spaces and an elevation of the g-ratio indicative of myelin sheath thinning in CADASIL WM.

Conclusion

Our findings suggest that accumulation of interstitial fluid and myelin damage are 2 major factors underlying early WM changes in CADASIL. Advanced diffusion MRI and relaxometry are promising approaches to decipher the underpinnings of WM alterations in SVDs.
Validation of Fourier transform infrared microspectroscopy for the evaluation of enzymatic cross-linking of bone collagen
Authors: Mieczkowska Aleksandra , Mabilleau Guillaume
Published: February 2023

Enzymatic cross-linking of the bone collagen is important to resist to crack growth and to increased flexural strength. In the present study, we proposed a new method for assessment of enzymatic cross-link based on FTIR microspectroscopy that takes into account secondary structure of type I collagen. Briefly, femurs were collected from sham or ovariectomized mice and subjected either to LC-MS or embedded in polymethylmethacrylate, cut and analyzed by FTIR microspectroscopy. FTIR acquisition were recorded before and after UV exposure or acid treatment. In addition, femurs from a second animal study were used to compare gene expression ofPlod2andLoxenzymes and enzymatic cross-links determined by FTIR microspectroscopy.

We evidenced here that intensities and areas of subbands located at ∼1660 cm-1, ∼1680 cm-1and ∼1690 cm-1were positively and significantly associated with the concentration of pyridinoline (PYD), deoxypyridinoline (DPD) or immature dihydroxylysinonorleucine (DHLNL) / hydroxylysinonorleucine (HLNL) cross-links. Seventy-two hours exposure to UV light significantly reduced by ∼86% and ∼89% the intensity and area of the ∼1660 cm-1subband. Similarly, 24 hours of acid treatment significantly reduced by 78% and 76% the intensity and area of the ∼1690 cm-1subband.Plod2andLoxexpression were also positively associated to the signal of the ∼1660 cm-1and ∼1690 cm-1subbands.

In conclusion, our study provided a new method for decomposing the amide I envelope of bone section that positively correlates with PYD and immature collagen cross-links. This method allows for investigation of tissue distribution of enzymatic cross-links in bone section.
Induction of viral mimicry upon loss of DHX9 and ADAR1 in breast cancer cells
Authors: Cottrell Kyle A. , Ryu Sua , Torres Luisangely Soto , Schab Angela M. , Weber Jason D.
Published: February 2023

Detection of viral double-stranded RNA (dsRNA) is an important component of innate immunity. However, many endogenous RNAs containing double-stranded regions can be misrecognized and activate innate immunity. The interferon inducible ADAR1-p150 suppresses dsRNA sensing, an essential function for ADAR1 in many cancers, including breast. Although ADAR1-p150 has been well established in this role, the functions of the constitutively expressed ADAR1-p110 isoform are less understood. We used proximity labeling to identify putative ADAR1-p110 interacting proteins in breast cancer cell lines. Of the proteins identified, the RNA helicase DHX9 was of particular interest. Knockdown of DHX9 in ADAR1-dependent cell lines caused cell death and activation of the dsRNA sensor PKR. In ADAR1-independent cell lines, combined knockdown of DHX9 and ADAR1, but neither alone, caused activation of multiple dsRNA sensing pathways leading to a viral mimicry phenotype. Together, these results reveal an important role for DHX9 in suppressing dsRNA sensing by multiple pathways.
The antiphage defense system CBASS controls resistance and enables killing by antifolate antibiotics inVibrio cholerae
Authors: Brenzinger Susanne , Airoldi Martina , Ogunleye Adewale Joseph , Brochado Ana Rita
Published: February 2023

Toxic bacterial modules, in particular toxin-antitoxin (TA) systems, have been long sought-after for their antimicrobial potential, although with limited success1–6. Here we show that the cyclic-oligonucleotide-based antiphage signaling system (CBASS), another example of a toxic module, increases sensitivity to well-established antifolate antibiotics, interferes with their synergy, and ultimately enables bacterial lysis by antifolates - classic bacteriostatic antibiotics, inVibrio cholerae. We propose a molecular mechanism for the CBASS-antifolate interaction based on onset of cyclic-oligonucleotide production by the nucleotidyltransferase DncV upon folate depletion by antifolates. CBASS-antifolate interaction is specific to CBASS systems with closely related nucleotidyltransferases and similar folate binding. Altogether, our findings illustrate that toxic modules, such as the antiphage defense CBASS system, can dramatically impact antibiotic activity, and open the possibility that endogenous metabolites could also act as triggers/silencers of toxic modules under stress beyond antibiotic treatment, such as during phage infection, biofilm formation or disease environments.
A Conserved Requirement for RME-8/DNAJC13 in Neuronal Autolysosome Reformation
Authors: Swords Sierra , Jia Nuo , Norris Anne , Modi Jil , Cai Qian , Grant Barth D.
Published: February 2023

Autophagosomes fuse with lysosomes, forming autolysosomes that degrade engulfed cargo. To maintain lysosomal capacity, autolysosome reformation (ALR) must regenerate lysosomes from autolysosomes using a membrane tubule-based process. Maintaining lysosomal capacity is required to maintain proteostasis and cellular health, especially in neurons where lysosomal dysfunction has been repeatedly implicated in neurodegenerative disease. Cell biological studies have linked the DNA-J domain Hsc70 co-chaperone RME-8/DNAJC13 to endosomal coat protein regulation, while human genetics studies have linked RME-8/DNAJC13 to neurological disease, including Parkinsonism and Essential Tremor. We report new analysis of the requirements for the RME-8/DNAJC13 protein in neurons, focusing onC. elegansmechanosensory neurons in the intact animal, and in primary mouse cortical neurons in culture. We find that loss of RME-8/DNAJC13 in both systems results in accumulation of grossly elongated autolysosomal tubules. FurtherC. elegansanalysis revealed a similar autolysosome tubule accumulation defect in mutants known to be required for ALR in mammals, including bec-1/beclin and vps-15/PIK3R4/p150 that regulate type-III PI3-kinase VPS-34, and dyn-1/dynaminthat severs ALR tubules. Clathrin is also an important ALR regulator implicated in autolysosome tubule formation and release. InC. eleganswe found that loss of RME-8 causes severe depletion of clathrin from neuronal autolysosomes, a phenotype shared withbec-1andvps-15mutants. We conclude that RME-8/DNAJC13 plays a conserved but previously unrecognized role in autolysosome reformation, likely affecting ALR tubule initiation and/or severing. Additionally, in both systems, we found that loss of RME-8/DNAJC13 appeared to reduce autophagic flux, suggesting feedback regulation from ALR to autophagy. Our results connecting RME-8/DNAJC13 to ALR and autophagy provide a potential mechanism by which RME-8/DNAJC13 could influence neuronal health and the progression of neurodegenerative disease.
Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
Authors: Karl Julie A. , Prall Trent M. , Bussan Hailey E. , Varghese Joshua M. , Pal Aparna , Wiseman Roger W. , O'Connor David H.
Published: February 2023

Macaques provide the most widely used nonhuman primate models for studying the immunology and pathogenesis of human diseases. Although the macaque major histocompatibility complex (MHC) region shares most features with the human leukocyte antigen (HLA) region, macaques have an expanded repertoire of MHC class I genes. Although a chimera of two rhesus macaque MHC haplotypes was first published in 2004, the structural diversity of MHC genomic organization in macaques remains poorly understood owing to a lack of adequate genomic reference sequences. We used ultralong Oxford Nanopore and high-accuracy Pacific Biosciences (PacBio) HiFi sequences to fully assemble the ∼5.2-Mb M3 haplotype of an MHC-homozygous, Mauritian-origin cynomolgus macaque (Macaca fascicularis). The MHC homozygosity allowed us to assemble a single MHC haplotype unambiguously and avoid chimeric assemblies that hampered previous efforts to characterize this exceptionally complex genomic region in macaques. The high quality of this new assembly is exemplified by the identification of an extended cluster of sixMafa-AGgenes that contains a recent duplication with a highly similar ∼48.5-kb block of sequence. The MHC class II region of this M3 haplotype is similar to the previously sequenced rhesus macaque haplotype and HLA class II haplotypes. The MHC class I region, in contrast, contains 13MHC-Bgenes, fourMHC-Agenes, and threeMHC-Egenes (vs. 19MHC-B, twoMHC-A, and oneMHC-Ein the previously sequenced haplotype). These results provide an unambiguously assembled single contiguous cynomolgus macaque MHC haplotype with fully curated gene annotations that will inform infectious disease and transplantation research.
How to reach a joint decision with the smallest need for compromise
Authors: Holguin Sofia , Kosheleva Olga
Published: February 2023

Purpose

Usually, people's interests do not match perfectly. So when several people need to make a joint decision, they need to compromise. The more people one has to coordinate the decision with, the fewer chances that each person's preferences will be properly taken into account. Therefore, when a large group of people need to make a decision, it is desirable to make sure that this decision can be reached by dividing all the people into small-size groups so that this decision can reach a compromise between the members of each group. The study's objective is to analyze when such a compromise is possible.

Design/methodology/approach

In this paper, the authors use a recent mathematical result about convex sets to analyze this problem and to come up with an optimal size of such groups.

Findings

The authors find the smallest group size for which a joint decision is possible. Specifically, the authors show that in situations where each alternative is characterized by n quantities, it is possible to have a joint decision if the participants are divided into groups of size n -- and, in general, no such decision is possible if the participants are divided into groups of size n -- 1.

Originality/value

The main novelty of this paper is that, first, it formulates the problem, which, to the best of the authors’ knowledge, was never formulated in this way before, and, second, that it provides a solution to this problem.
Adaptability of enterprise resource planning (ERP) systems for cost management of building construction projects in Sri Lanka
Authors: Jayamaha B.H.V.H. , Perera B.A.K.S. , Gimhani K.D.M. , Rodrigo M.N.N.
Published: February 2023

Purpose

Enterprise resource planning (ERP) systems that are equipped with numerous features and functionalities help to improve the profitability of construction corporations around the world through enhancing the efficiency of the functions related to cost management. Thus, the purpose of this study was to investigate the applicability of ERP systems for cost management of building construction projects in Sri Lanka.

Design/methodology/approach

A qualitative technique was used in this study, which comprised two-round Delphi-based semistructured interviews. Purposive sampling was used to determine the interviewees. Content analysis was used to evaluate the collected data.

Findings

The findings of this study identified the ERP system as a strategic tool for gaining a competitive advantage for an organization while confirming 14 uses of ERP systems and 16 stages of the cost management process. Eighteen issues were finalized at the end of the interview rounds while categorizing the suitable ERP applications at each stage of the cost management process.

Originality/value

Even though there are numerous distinct studies conducted on cost management and ERP systems, there has been a lack of studies conducted on the synergy between these two areas that can be adapted for the building projects in the Sri Lankan context. Therefore, the findings of this study can bring a new paradigm to the Sri Lankan construction sector by influencing the adaption of correct ERP systems at numerous project stages by providing a competitive edge.
Urban night lighting evaluation system and case study: blending popular contemporary elements, cultural traditions and advanced lighting technologies
Authors: Lin Qingcheng , Zhang Chi , Cai Huiling , Li Xuefeng , Xiao Hui
Published: February 2023

Purpose

Night lighting reflects the prosperous development of economic and the increasingly rich and colorful cultural life. Currently, various technical standards, protocols and management specifications have been developed to build a safe, comfortable and economical lighting environment. However, prevailing evaluation systems focus on objective indexes of illumination and have ignored environmental characteristics and subjective feelings and lacked consideration of regional culture, economic benefit, management and maintenance. In this context, a lighting evaluation system combining subjective and objective is proposed for the first time in this study to explore approaches to guide the development of a healthy and comfortable urban night-time environment.

Design/methodology/approach

Existing research and relevant lighting standards are analyzed and an evaluation model with a logical hierarchy is constructed by combining with the evaluation theory that is set based on people and the environment. The index weights were scientifically determined on the basis of the analytic hierarchy process (AHP) and fuzzy comprehensive evaluation method. The rationality and validity of the proposed evaluation system is verified in accordance with field projects and case studies.

Findings

Taking into account traditional and cultural factors, the evaluation model established has an acceptable accuracy. Evaluation based on subjective-objective combination can provide a scientific basis for the management and optimization of night lighting.

Originality/value

The proposed evaluation system can serve as a guiding reference for other areas of cultural identity and esthetic perspective.
Effects of coflow-jet active flow control on airfoil stall
Authors: Yazdani Shima , Salimipour Erfan , Salimipour Ayoob , Sheremet Mikhail A. , Ghalambaz Mohammad
Published: February 2023

Purpose

Active flow control on the NACA 0024 airfoil defined as suction-injection jet at the chord-based Reynolds number of 1.5 × 1e + 5 is studied.

Design/methodology/approach

The three-dimensional incompressible unsteady Reynolds-averaged Navier–Stokes equations with the SST k-ω turbulence model are used to study the effects of coflow-jet (CFJ) on the dynamic and static stall phenomena. CFJ implementation is conducted with several momentum coefficients to investigate their turnover. Furthermore, the current work intends to analyze the CFJ performance by varying the Reynolds number and jet momentum coefficient and comparing all states to the baseline airfoil, which has not been studied in prior research investigations.

Findings

It is observed that at the momentum coefficient (Cµ) of 0.06, the lift coefficients at low attack angles (up to a = 15) dramatically increase. Furthermore, the dynamic stall at the given Reynolds number and with the lowered frequency of 0.15 is explored. In the instance of Cµ = 0.07, the lift coefficient curve does not show a noticeable stall feature compared to Cµ = 0.05, suggesting that a more powerful stronger jet can entirely control the dynamic stall.

Originality/value

Furthermore, the current work intends to analyze the CFJ performance by varying the jet momentum coefficient and comparing all states to the baseline airfoil, which has not been studied in prior research investigations.
The potential of 3D printing in building pathology: rehabilitation of cultural heritage
Authors: Jesus Manuel , Guimarães Ana Sofia , Rangel Bárbara , Lino Alves Jorge
Published: February 2023

Purpose

The paper seeks to bridge the already familiar benefits of 3D printing (3DP) to the rehabilitation of cultural heritage, still based on the use of complex and expensive handcrafted techniques and scarce materials.

Design/methodology/approach

A compilation of different information on frequent anomalies in cultural heritage buildings and commonly used materials is conducted; subsequently, some innovative techniques used in the construction sector (3DP and 3D scanning) are addressed, as well as some case studies related to the rehabilitation of cultural heritage building elements, leading to a reflection on the opportunities and challenges of this application within these types of buildings.

Findings

The compilation of information summarised in the paper provided a clear reflection on the great potential of 3DP for cultural heritage rehabilitation, requiring the development of new mixtures (lime mortars, for example) compatible with the existing surface and, eventually, incorporating some residues that may improve interesting properties; the design of different extruders, compatible with the new mixtures developed and the articulation of 3D printers with the available mapping tools (photogrammetry and laser scanning) to reproduce the component as accurately as possible.

Originality/value

This paper sets the path for a new application of 3DP in construction, namely in the field of cultural heritage rehabilitation, by identifying some key opportunities, challenges and for designing the process flow associated with the different technologies involved.