bluuebunny/crossref_metadata_2025 huggingface dataset:
Back to the Basics: An Alternative Approach to ABG Interpretation
Authors: Nguyen Emily , Turpin Chase , deLuna Andres
Published: August 2023

Medical education has promoted the rapid interpretation of the arterial blood gas (ABG) as a crucial skill in the management of critically ill patients. The first step of many algorithms focuses on using log-linear estimates to determine the internal consistency of ABG values. However, because of modern computing advances, these estimates are no longer necessary. We demonstrate an alternative method for ascertaining internal consistency of ABG values based on direct calculation derived directly from Henderson-Hasselbach and demonstrate its efficiency and accuracy.

Deidentified ABG values were collected from electronic medical records for the month of September 2022. Estimated hydrogen concentration was calculated by log linear estimation and by the proposed method of direct calculation. Time of computation, a measure of efficiency, was also recorded.

Of the 1008 ABGs used for analysis, 185 (18.4%) had estimated hydrogen concentrations that were greater than a 5% threshold according to the guidelines method, suggesting potential internal inconsistency. However, only 13 (1.3%) had estimated hydrogen concentrations greater than 5% by direct calculation. Analysis was also performed at a 10% threshold. On further analysis, 4 ABGs that were identified by the guidelines method as being internally inconsistent, but not identified by the direct calculation method, were found to have pH <7.0, outside the range provided for the current guidelines for log-linear estimation, and were thus incorrectly identified by the guidelines method as being internally inconsistent. The time of computation for direct calculation was approximately 8-fold faster, although the total time of calculation for this dataset was minimal.

This study demonstrates a direct calculation method as an alternative approach to traditional guidelines to assess internal ABG value consistency, the first step of ABG interpretation. We demonstrate that direct calculation is more accurate, identifying less potentially internally inconsistent values, notably at extremes in pH. In addition, the direct calculation algorithm is 8-fold more efficient than guidelines-based algorithm, although actual processing times were miniscule for the data set regardless of the method used. Furthermore, with modern calculators and computers, the direct calculation method is easier to understand and implement than the guideline based approach. Therefore, based on the results of this study, we propose the use of direct calculation as an alternative to log-linear based estimation for the assessment of internal consistency of ABGs.
DNL343 is an investigational CNS penetrant eIF2B activator that prevents and reverses the effects of neurodegeneration caused by the Integrated Stress Response
Authors: Yulyaningsih Ernie , Suh Jung H. , Fanok Melania H. , Chau Roni , Solanoy Hilda , Takahashi Ryan , Bakardjiev Anna I. , Becerra Isabel , Benitez N. Butch , Chiu Chi-Lu , Davis Sonnet S , Dowdle William E. , Earr Timothy , Estrada Anthony A. , Gill Audrey , Ha Connie , Haddick Patrick C. G. , Henne Kirk R. , Larhammar Martin , Leung Amy Wing-Sze , Maciuca Romeo , Memarzadeh Bahram , Nguyen Hoang N. , Nugent Alicia , Osipov Maksim , Ran Yingqing , Rebadulla Kevin , Roche Elysia , Sandmann Thomas , Wang Jing , Lewcock Joseph W. , Scearce-Levie Kimberly , Kane Lesley A. , Sanchez Pascal E.
Published: August 2023

The integrated stress response (ISR) is a conserved pathway in eukaryotic cells that is activated in response to multiple sources of cellular stress. Although acute activation of this pathway restores cellular homeostasis, intense or prolonged ISR activation perturbs cell function and may contribute to neurodegeneration. DNL343 is an investigational CNS-penetrant small molecule ISR inhibitor designed to activate the eukaryotic initiation factor 2B (eIF2B) and suppress aberrant ISR activation. DNL343 reduced CNS ISR activity and neurodegeneration in a dose-dependent manner in two establishedin vivomodels – the optic nerve crush injury and an eIF2B loss of function (LOF) mutant – demonstrating neuroprotection in both and preventing motor dysfunction in the LOF mutant mouse. Treatment with DNL343 at a late stage of disease in the LOF model reversed elevation in plasma biomarkers of neuroinflammation and neurodegeneration and prevented premature mortality. Several proteins and metabolites that are dysregulated in the LOF mouse brains were normalized by DNL343 treatment, and this response is detectable in human biofluids. Several of these biomarkers show differential levels in CSF and plasma from patients with vanishing white matter disease (VWMD), a neurodegenerative disease that is driven by eIF2B LOF and chronic ISR activation, supporting their potential translational relevance. This study demonstrates that DNL343 is a brain penetrant ISR inhibitor capable of attenuating neurodegeneration in mouse models and identifies several biomarker candidates that may be used to assess treatment responses in the clinic.
The odor of a nontoxic tetrodotoxin analog, 5,6,11-trideoxytetrodotoxin, is detected by specific olfactory sensory neurons of the green spotted puffers
Authors: Suzuki Takehisa , Nakahigashi Ryota , Adachi Masaatsu , Nishikawa Toshio , Abe Hideki
Published: August 2023

Toxic puffers accumulate tetrodotoxin (TTX), a well-known neurotoxin, by feeding on TTX-bearing organisms and using it to defend themselves from predators. Our previous studies have demonstrated that toxic puffers are attracted to 5,6,11-trideoxytetrodotoxin (TDT), a nontoxic TTX analog that is simultaneously accumulated with TTX in toxic puffers and their prey. In addition, activity labeling using immunohistochemistry targeting neuronal activity marker suggests that TDT activates crypt olfactory sensory neurons (OSN) of the green spotted puffer. However, it remains to be determined whether individual crypt OSNs can physiologically respond to TDT. By employing electroporation to express GCaMP6s in OSNs, we successfully identified a distinct group of oval OSNs that exhibited a specific calcium response when exposed to TDT in green spotted puffers. These oval OSNs showed no response to amino acids (AAs), which serve as food odor cues for teleosts. Furthermore, oval morphology and surface positioning of TDT-sensitive OSNs in the olfactory epithelium closely resemble that of crypt OSNs. These findings further substantiate that TDT is specifically detected by crypt OSNs in green spotted puffer. The TDT odor may act as a chemoattractant for finding conspecific toxic puffers and for feeding TTX-bearing organisms for effective toxification.
“Role of a Pdlim5:PalmD complex in directing dendrite morphology”
Authors: Srivastava Yogesh , Donta Maxsam , Mireles Lydia L. , Paulucci-Holthauzen Adriana , Waxham M. Neal , McCrea Pierre D.
Published: August 2023

Neuronal connectivity is regulated during normal brain development with the arrangement of spines and synapses being dependent on the morphology of dendrites. Further, in multiple neurodevelopmental and aging disorders, disruptions of dendrite formation or shaping is associated with atypical neuronal connectivity. We showed previously that Pdlim5 binds delta-catenin and promotes dendrite branching (Baumert et al.,J Cell Biol2020). We report here that Pdlim5 interacts with PalmD, a protein previously suggested by others to interact with the cytoskeleton (e.g.,viaadducin/spectrin) and to regulate membrane shaping. Functionally, the knockdown of PalmD or Pdlim5 in rat primary hippocampal neurons dramatically reduces branching and conversely, PalmD exogenous expression promotes dendrite branching as does Pdlim5. Further, we show that each proteins’ effects are dependent on the presence of the other. In summary, using primary rat hippocampal neurons we reveal the contributions of a novel Pdlim5:PalmD protein complex, composed of functionally inter-dependent components responsible for shaping neuronal dendrites.
A phylogenetic approach to explore theAspergillus fumigatusconidial surface-associated proteome and its role in pathogenesis
Authors: Valero Clara , Pinzan Camila Figueiredo , de Castro Patrícia Alves , van Rhijn Norman , Earle Kayleigh , Liu Hong , Horta Maria Augusta Crivelente , Kniemeyer Olaf , Krüger Thomas , Pschibul Annica , Coemert Derya Nur , Heinekamp Thorsten , Brakhage Axel A. , Steenwyk Jacob L. , Mead Matthew E. , Rokas Antonis , Filler Scott G. , da Rosa-Garzon Nathalia Gonsales , Cabral Hamilton , Deljabe Endrews , Bromley Michael J. , Angeli Claudia B. , Palmisano Giuseppe , Ibrahim Ashraf S , Gago Sara , dos Reis Thaila F. , Goldman Gustavo H.
Published: August 2023

Aspergillus fumigatus, an important pulmonary fungal pathogen causing several diseases collectively called aspergillosis, relies on asexual spores or conidia for initiating host infection. Here, we used a phylogenomic approach to compare proteins in the conidial surface ofA. fumigatus, two closely related non-pathogenic species,Aspergillus fischeriandAspergillus oerlinghausenensis, and the cryptic pathogenAspergillus lentulus. After identifying 62 proteins uniquely expressed on theA. fumigatusconidial surface, we deleted 42 genes encoding conidial proteins. We found deletion of 33 of these genes altered susceptibility to macrophage killing, penetration and damage to epithelial cells, and cytokine production. Notably, a gene that encodes glycosylasparaginase, which modulates levels of the host pro-inflammatory cytokine IL-1β, is important for infection in an immunocompetent murine model of fungal disease. These results suggest thatA. fumigatusconidial surface proteins and effectors are important for evasion and modulation of the immune response at the onset of fungal infection.
Critical factors for precise and efficient RNA cleavage by RNase Y inStaphylococcus aureus
Authors: Le Scornet Alexandre , Jousselin Ambre , Baumas Kamila , Kostova Gergana , Durand Sylvain , Poljak Leonora , Barriot Roland , Coutant Eve , Pigearias Romain , Tejero Gabriel , Lootvoet Jonas , Péllisier Céline , Munoz Gladys , Condon Ciarán , Redder Peter
Published: August 2023

Cellular processes require precise and specific gene regulation, in which continuous mRNA degradation is a major element. The mRNA degradation mechanisms should be able to degrade a wide range of different RNA substrates with high efficiency, but should at the same time be limited, to avoid killing the cell by elimination of all cellular RNA. RNase Y is a major endoribonuclease found in most Firmicutes, includingBacillus subtilisandStaphylococcus aureus. However, the molecular interactions that direct RNase Y to cleave the correct RNA molecules at the correct position remain unknown. In this work we have identified transcripts that are homologs inS. aureusandB. subtilis, and are RNase Y targets in both bacteria. Two such transcript pairs were used as models to show a functional overlap between theS. aureusand theB. subtilisRNase Y, which highlighted the importance of the nucleotide sequence of the RNA molecule itself in the RNase Y targeting process. Cleavage efficiency is driven by the primary nucleotide sequence immediately downstream of the cleavage site and base-pairing in a secondary structure a few nucleotides downstream. Cleavage positioning is roughly localised by the downstream secondary structure and fine-tuned by the nucleotide immediately upstream of the cleavage. The identified elements were sufficient for RNase Y-dependent cleavage, since the sequence elements from one of the model transcripts were able to convert an exogenous non-target transcript into a target for RNase Y.

Author summary

In order to correctly regulate the level of RNAs, bacteria require their RNA to be continuously synthesised and degraded. However, even related bacterial species can have different sets of ribonucleases, each with their own target criteria. Here we explore which sequence elements of an RNA are important for being targeted by the endoribonuclese RNase Y in the two bacteria,Staphylococcus aureusandBacillus subtilis. We specifically examine the RNase Y dependent cleavage of two transcripts that have homologs in both bacteria. We identify a short single-stranded regions immediately downstream of the cleavage position can be modified to change the cleavage efficiency up to 20-fold. We furthermore discover that a secondary structure a few nucleotides downstream of the cleavage is required for cleavage and that the positioning of the cleavage can be modulated by moving this structure.
PRO-LDM: Protein Sequence Generation with a Conditional Latent Diffusion Model
Authors: Zhang Sitao , Jiang Zixuan , Huang Rundong , Mo Shaoxun , Zhu Letao , Li Peiheng , Zhang Ziyi , Pan Emily , Chen Xi , Long Yunfei , Liang Qi , Tang Jin , Xu Renjing , Qing Rui
Published: August 2023

Abstracts

Deep learning-driven protein design holds enormous potential despite the complexities in sequences and structures. Recent developments in diffusion models yielded success in structure design, but awaits progress in sequence design and are computationally demanding. Here we present PRO-LDM: an efficient framework combining design fidelity and computational efficiency, utilizing the diffusion model in latent space to design proteins with property tuning. The model employs a joint autoencoder to capture latent variable distributions and generate meaningful embeddings from sequences. PRO-LDM (1) learns representations from biological features in natural proteins at both amino-acid and sequence level; (2) generates native-like new sequences with enhanced diversity; and (3) conditionally designs new proteins with tailored properties or functions. The out-of-distribution design enables sampling notably different sequences by adjusting classifier guidance strength. Our model presents a feasible pathway and an integratable tool to extract physicochemical and evolutionary information embedded within primary sequences, for protein design and optimization.
Brief and diverse excitotoxic insults cause an increase in neuronal nuclear membrane permeability in the neonatal brain
Authors: Suryavanshi P. , Langton R. , Fairhead K. , Glykys J.
Published: August 2023

Neuronal swelling after excitotoxic insults is implicated in neuronal injury and death in the developing brain, yet mitigating brain edema with osmotic and surgical interventions yields poor clinical outcomes. Importantly, neuronal swelling and its downstream consequences during early brain development remain poorly investigated. Using multiphoton Ca2+imagingin vivo(P12-17) and in acute brain slices (P8-12), we explored Ca2+-dependent downstream effects after neuronal cytotoxic edema. We observed the translocation of cytosolic GCaMP6s into the nucleus of a subpopulation of neurons minutes after various excitotoxic insults. We used automated morphology-detection algorithms for neuronal segmentation and quantified the nuclear translocation of GCaMP6s as the ratio of nuclear and cytosolic intensity (N/C ratio). Elevated neuronal N/C ratios were correlated to higher Ca2+loads and could occur independently of neuronal swelling. Electron microscopy revealed that the nuclear translocation was associated with increased nuclear pore size. Inhibiting calpains prevented elevated N/C ratios and neuronal swelling. Thus, our results indicate altered nuclear transport in a subpopulation of neurons shortly after injury in the developing brain, which can be used as an early biomarker of acute neuronal injury.
The ventral tegmental area dopamine to lateral amygdala projection supports cocaine cue associative learning
Authors: Smith Dana M. , Torregrossa Mary M.
Published: August 2023

Learning and memory mechanisms are critically involved in drug craving and relapse. Environmental cues paired with repeated drug use acquire incentive value such that exposure to the cues alone can trigger craving and relapse. The amygdala, particularly the lateral amygdala (LA), underlies cue-related learning processes that assign valence to environmental stimuli including drug-paired cues. Evidence suggests that the ventral tegmental area (VTA) dopamine (DA) projection to the LA participates in encoding reinforcing effects that act as a US in conditioned cue reward-seeking as DA released in the amygdala is important for emotional and behavioral functions. Here we used chemogenetics to manipulate these VTA DA inputs to the LA to determine the role of this projection for acquisition of drug-cue associations and reinstatement of drug-seeking. We found inhibiting DA input to the LA during cocaine self-administration slowed acquisition and weakened the ability of the previously cocaine-paired cue to elicit cocaine-seeking. Conversely, exciting the projection during self-administration boosted the salience of the cocaine-paired cue as indicated by enhanced responding during cue-induced reinstatement. Importantly, interfering with DA input to the LA had no impact on the ability of cocaine to elicit a place preference or induce reinstatement in response to a priming cocaine injection. Overall, we show that manipulation of projections underlying DA signaling in the LA may be useful for developing therapeutic interventions for substance use disorders.
Extreme high-elevation mammal surveys reveal unexpectedly high upper range limits of Andean mice
Authors: Storz Jay F. , Quiroga-Carmona Marcial , Liphardt Schuyler , Bautista Naim M. , Opazo Juan C. , Rico Cernohorska Adriana , Salazar-Bravo Jorge , Good Jeffrey M. , D’Elía Guillermo
Published: August 2023

In the world’s highest mountain ranges, uncertainty about the upper elevational range limits of alpine animals represents a critical knowledge gap regarding the environmental limits of life and presents a problem for detecting range shifts in response to climate change. Here we report results of mountaineering mammal surveys in the Central Andes, which led to the discovery of multiple species of mice living at extreme elevations that far surpass previously assumed range limits for mammals. We live-trapped small mammals from ecologically diverse sites spanning >6700 m of vertical relief, from the desert coast of northern Chile to the summits of the highest volcanoes in the Andes. We used molecular sequence data and whole-genome sequence data to confirm the identities of species that represent new elevational records and to test hypotheses regarding species limits. These discoveries contribute to a new appreciation of the environmental limits of vertebrate life.
Preclinical evaluation of the efficacy and safety of AAV1-hOTOF in mice and non-human primates
Authors: Zhang Longlong , Wang Hui , Xun Mengzhao , Tang Honghai , Wang Jinghan , Lv Jun , Zhu Biyun , Chen Yuxin , Wang Daqi , Hu Shaowei , Gao Ziwen , Liu Jianping , Chen Zheng-Yi , Chen Bing , Li Huawei , Shu Yilai
Published: August 2023

Pathogenic mutations in theOTOFgene cause autosomal recessive hearing loss 9 (DFNB9), one of the most common forms of auditory neuropathy. There is no biological treatment for DFNB9. Here, we designed anOTOFgene therapy agent by dual AAV1 carrying humanOTOFcoding sequences with the expression driven by the hair cell-specific promoterMyo15, AAV1-hOTOF. To develop a clinical application of AAV1-hOTOF gene therapy, we evaluated its efficacy and safety in animal models by pharmacodynamics, behavior, and histopathology. AAV1-hOTOF inner ear delivery significantly improved hearing inOtof−/−mice without affecting normal hearing in wild-type mice. AAV1 was predominately distributed to the cochlea although it was detected in other organs such as the central nervous system and the liver, and no obvious toxic effects of AAV1-hOTOF were observed in mice. To further evaluate the safety ofMyo15promoter-driven AAV1-transgene, AAV1-GFP was delivered into the inner ear ofMacaca fascicularisvia the round window membrane. AAV1-GFP transduced 60-94% of the inner hair cells along the cochlear turns. AAV1-GFP was detected in isolated organs and no significant adverse effects were detected. These results suggest that AAV1-hOTOF is well tolerated and effective in animals, providing critical support for its clinical translation.
Overestimation in time reproduction: Influences of accuracy feedback and attentional sharing
Authors: Chen Lingyue , Shi Zhuanghua
Published: August 2023

Duration reproduction is often subjective to biases, with a general tendency to overestimate durations, which has been observed in many studies. Yet, this overestimation is frequently dismissed as a nuisance error, and its underlying mechanisms remain elusive. Here, we conducted two experiments to investigate this general overestimation in duration reproduction. To pin down the origin of the error, we manipulated the reproduction output through shortened visual feedback in Experiment 1, while varying the presence of accuracy feedback in Experiment 2. Across both experiments, we observed a consistent overestimation in reproduction when accuracy feedback was absent. This overestimation, amounting to approximately 13.5% on a ratio basis across different durations and sessions, was unaffected by shortened visual feedback. We propose that this consistent overestimation is likely due to the attentional sharing between the action execution and the monitoring of the passage of time during the reproduction process.
Apoptosis-mediated ADAM10 activation removes a mucin barrier promoting T cell efferocytosis
Authors: Drexhage Linnea Z. , Zhang Shengpan , DuPont Maeva , Ragaller Franziska , Sjule Ellen , Caballero Jose Cabezas , Deimel Lachlan , Robertson Helen , Russell Rebecca A , Dushek Omer , Sezgin Erdinc , Karaji Niloofar , Sattentau Quentin J
Published: August 2023

Efferocytic clearance of apoptotic cells in general, and T cells in particular, is required for tissue and immune homeostasis. Transmembrane mucins are extended glycoproteins highly expressed in the cell glycocalyx that act as a barrier to phagocytosis. Whether and how mucins may be regulated during cell death to facilitate efferocytic corpse clearance is not understood. Here we show that normal and transformed human T cells express a subset of mucins which are rapidly and selectively removed from the cell surface during apoptosis. This process is mediated by the ADAM10 sheddase, the activity of which is associated with XKR8-catalyzed flipping of phosphatidylserine to the outer leaflet of the plasma membrane. Mucin clearance enhances uptake of apoptotic T cells by macrophages, confirming mucins as an enzymatically-modulatable barrier to efferocytosis. Together these findings reveal a novel glycocalyx regulatory pathway with implications for therapeutic intervention in the clearance of normal and transformed apoptotic T cells.
Loss-of-function cancer-associated mutations in the EIF4G2 non-canonical translation initiation factor
Authors: Meril Sara , Bahlsen Marcela , Eisenstein Miriam , Savidor Alon , Levin Yishai , Bialik Shani , Pietrokovski Shmuel , Kimchi Adi
Published: August 2023

Tumor cells often exploit the protein translation machinery, resulting in enhanced protein expression essential for tumor growth. Since canonical translation initiation is often suppressed due to cell stress in the tumor microenvironment, non-canonical translation initiation mechanisms become particularly important for shaping the tumor proteome. EIF4G2 is a non-canonical translation initiation factor that mediates internal ribosome entry site [IRES] and upstream open reading frame [uORF] dependent initiation mechanisms, which can be used to modulate protein expression in cancer. Here we explored the contribution of EIF4G2 to cancer by screening the COSMIC database for EIF4G2 somatic mutations in cancer patients. Functional examination of missense mutations revealed deleterious effects on EIF4G2 protein-protein interactions, and importantly, on its ability to mediate non-canonical translation initiation. Specifically, one mutation, R178Q, led to reductions in protein expression and near complete loss-of-function. Two other mutations within the MIF4G domain specifically affected EIF4G2’s ability to mediate IRES-dependent translation initiation but not that of target mRNAs with uORFs. These results shed light on both the structure-function of EIF4G2 and its potential tumor suppressor effects.
The three-dimensionally articulated oral apparatus of a Devonian heterostracan sheds light on feeding in Palaeozoic jawless fishes
Authors: Dearden Richard , Jones Andy , Giles Sam , Lanzetti Agnese , Grohganz Madleen , Johanson Zerina , Lautenschlager Stephan , Randle Emma , Donoghue Philip C. J. , Sansom Ivan J.
Published: August 2023

Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is preserved only in the early diverging stem-gnathostome heterostracans and its anatomy remains poorly understood. Here we use X-ray microtomography to characterise the feeding apparatus of the pteraspid heterostracanRhinopteraspis dunensis(Roemer, 1855). We show that the apparatus is composed of thirteen plates arranged approximately bilaterally, the majority of which articulate from the postoral plate. Our reconstruction of the apparatus shows that the oral plates would have been capable of movement within the dorso-ventral plane, but their degree of movement was limited. The functional morphology of the apparatus inRhinopteraspisprecludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterised by a directional trend towards increasingly active food acquisition.
Fatty acid desaturation and lipoxygenase pathways support trained immunity
Authors: Ferreira Anaísa V. , Alarcon-Barrera Juan Carlos , Domínguez-Andrés Jorge , Bulut Ozlem , Kilic Gizem , Debisarun Priya A. , Röring Rutger J. , Özhan Hatice N. , Terschlüsen Eva , Ziogas Athanasios , Kostidis Sarantos , Mohammed Yassene , Matzaraki Vasiliki , Renieris George , Giamarellos-Bourboulis Evangelos J , Netea Mihai G. , Giera Martin
Published: August 2023

Infections and vaccinations can induce long-term enhanced responses of innate immune cells to heterologous stimuli, establishing ade factoinnate immunological memory termedtrained immunity. Monocytes exposed to the Bacillus Calmette-Guérin (BCG) vaccine, have a trained immunity phenotype, characterized by an increased biosynthesis of different lipid mediators (LMs) derived from long-chain polyunsaturated fatty acids (PUFAs). Pharmacological and genetic approaches showed that long-chain PUFA synthesis and lipoxygenase (LOX)-derived LMs are crucial for the BCG trained immunity responses of human monocytes. Furthermore, monocytes of healthy individuals vaccinated with BCG are enriched in 12-LOX products. The elucidation of the lipid metabolic pathways that promote innate immune memory contributes to our understanding of trained immunity and may help identify therapeutic tools and targets for the modulation of innate immune responses.
Critical importance of DNA binding for CSL protein functions in fission yeast
Authors: Marešová Anna , Oravcová Martina , Hradilová Miluše , Zemlianski Viacheslav , Häsler Robert , Převorovský Martin
Published: August 2023

CSL (CBF1/RBP-Jκ/Suppressor of Hairless/LAG-1) proteins are conserved transcription factors found in animals and fungi. In fission yeast, they regulate various cellular processes, including cell cycle progression, lipid metabolism, and cell adhesion. CSL proteins bind to DNA through their N-terminal Rel-like domain and central beta-trefoil domain. Here, we investigated the importance of DNA binding for CSL functions in the fission yeastSchizosaccharomyces pombe. We created CSL mutants with disrupted DNA binding and found that the vast majority of CSL functions depend on intact DNA binding. Specifically, DNA binding is crucial for the regulation of cell adhesion, lipid metabolism, cell cycle progression, long non-coding RNA expression, and genome integrity maintenance. Interestingly, perturbed lipid metabolism leads to chromatin structure changes, potentially linking lipid metabolism to the diverse CSL-associated phenotypes. Our study highlights the critical role of DNA binding for CSL protein functions in fission yeast.

SUMMARY STATEMENT

CSL transcription factors regulate a diverse set of processes, but the mechanisms are not always clear. We show thatS. pombeCSL proteins need the ability to bind DNA for most of their roles.
Integrating habitat suitability modeling with gene flow improves delineation of landscape connections among African savanna elephants
Authors: de Flamingh Alida , Alexander Nathan , Perrin-Stowe Tolulope I.N. , Donnelly Cassidy , Guldemondt Robert A.R. , Schooley Robert L. , van Aarde Rudi J. , Roca Alfred L.
Published: August 2023

Across Africa, space for conservation is sometimes limited to formally protected areas that have become progressively more isolated. There is a need for targeted conservation initiatives such as the demarcation of landscape connections, defined as areas that encompass environmental variables that promote the natural movement of individuals between populations, which can facilitate gene flow. Landscape connections can mitigate genetic isolation, genetic drift, and inbreeding, which can occur in isolated populations in protected areas. Promoting gene flow can reduce the risk of extirpation often associated with isolated populations. Here we develop and test models for identifying landscape connections among African savannah elephant (Loxodonta africana) populations by combining habitat suitability modeling with gene flow estimates across a large region including seven countries. We find a pronounced non-linear response to unsuitable habitat, consistent with previous studies showing that non-transformed habitat models are poor predictors of gene flow. We generated a landscape connections map that considers both suitable habitats based on telemetry occurrence data and gene flow estimated as the inverse of individual genetic distance, delineating areas that are important for maintaining elephant population connectivity. Our approach represents a novel framework for developing spatially and genetically informed conservation strategies for elephants and many other taxa distributed across heterogeneous and fragmented landscapes.

GRAPHICAL ABSTRACT
Turnover of retroelements and satellite DNA drives centromere reorganization over short evolutionary timescales in Drosophila
Authors: Courret Cécile , Hemmer Lucas W. , Wei Xiaolu , Patel Prachi D. , Chabot Bryce J. , Fuda Nicholas J. , Geng Xuewen , Chang Ching-Ho , Mellone Barbara , Larracuente Amanda M.
Published: August 2023

Centromeres reside in rapidly evolving, repeat-rich genomic regions, despite their essential function in chromosome segregation. Across organisms, centromeres are rich in selfish genetic elements such as transposable elements and satellite DNAs that can bias their transmission through meiosis. However, these elements still need to cooperate at some level and contribute to, or avoid interfering with, centromere function. To gain insight into the balance between conflict and cooperation at centromeric DNA, we take advantage of the close evolutionary relationships within theDrosophila simulansclade –D. simulans, D. sechellia,andD. mauritiana –and their relative,D. melanogaster. Using chromatin profiling combined with high resolution fluorescence in situ hybridization on stretched DNA, we characterize all centromeres across these species. We discovered dramatic centromere reorganization involving recurrent shifts between retroelements and satellite DNAs over short evolutionary timescales. We also reveal the recent origin (<240 Kya) of telocentric chromosomes inD. sechellia,where the X and 4thcentromeres now sit on telomere-specific retroelements. Finally, the Y chromosome centromeres, which are the only chromosomes that do not experience female meiosis, do not show dynamic cycling between satDNA and TEs. The patterns of rapid centromere turnover in these species are consistent with genetic conflicts in the female germline and have implications for centromeric DNA function and karyotype evolution. Regardless of the evolutionary forces driving this turnover, the rapid reorganization of centromeric sequences over short evolutionary timescales highlights their potential as hotspots for evolutionary innovation.
Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins
Authors: Yang Zhimin , Stein Richard A. , Pink Maren , Madzelan Peter , Ngendahimana Thacien , Rajca Suchada , Wilson Mark A. , Eaton Sandra S. , Eaton Gareth R. , Mchaourab Hassane S. , Rajca Andrzej
Published: August 2023

We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water,Ka= 1.9 × 106M-1, is at least one order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase of the rotational correlation time,τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase inτrotand electron spin coherence time,Tm, along with the narrowing of inter-spin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4 – 9, compared to the common spin label such as MTSL, which is not affected by CB-7. Inter-spin distances of 3-nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating undisturbed structure and conformation of the protein.

Abstract Figure
Morphological hallmarks of dopaminergic neurodegeneration are associated with altered neuron function inCaenorhabditis elegans
Authors: Clark Andrew S. , Huayta Javier , Morton Katherine S. , Meyer Joel N. , San-Miguel Adriana
Published: August 2023

Caenorhabditis elegans(C. elegans) is an excellent model system to study neurodegenerative diseases, such as Parkinson’s disease, as it enables analysis of both neuron morphology and function in live animals. Multiple structural changes in neurons, such as cephalic dendrite morphological abnormalities, have been considered hallmarks of neurodegeneration in this model, but their relevance to changes in neuron function are not entirely clear. We sought to test whether hallmark morphological changes associated with chemically induced dopaminergic neuron degeneration, such as dendrite blebbing, breakage, and loss, are indicative of neuronal malfunction and result in changes in behavior. We adapted an established dopaminergic neuronal function assay by measuring paralysis in the presence of exogenous dopamine, which revealed clear differences betweencat-2dopamine deficient mutants, wildtype worms, anddat-1dopamine abundant mutants. Next, we integrated an automated image processing algorithm and a microfluidic device to segregate worm populations by their cephalic dendrite morphologies. We show that nematodes with dopaminergic dendrite degeneration markers, such as blebbing or breakage, paralyze at higher rates in a dopamine solution, providing evidence that dopaminergic neurodegeneration morphologies are correlated with functional neuronal outputs.
REVEALS: An Open Source Multi Camera GUI For Rodent Behavior Acquisition
Authors: Phadke Rhushikesh A. , Wetzel Austin M. , Fournier Luke A. , Sha Mingqi , Padró-Luna Nicole M. , Cruz-Martín Alberto
Published: August 2023

Understanding the rich behavioral data generated by mice is essential for deciphering the function of the healthy and diseased brain. However, the current landscape lacks effective, affordable, and accessible methods for acquiring such data, especially when employing multiple cameras simultaneously. We have developed REVEALS (Rodent BEhaVior Multi-camErA Laboratory AcquiSition), a graphical user interface (GUI) written in python for acquiring rodent behavioral data via commonly used USB3 cameras. REVEALS allows for user-friendly control of recording from one or multiple cameras simultaneously while streamlining the data acquisition process, enabling researchers to collect and analyze large datasets efficiently. We release this software package as a stand-alone, open-source framework for researchers to use and modify according to their needs. We describe the details of the GUI implementation, including the camera control software and the video recording functionality. We validate results demonstrating the GUI’s stability, reliability, and accuracy for capturing and analyzing rodent behavior using DeepLabCut pose estimation in both an object and social interaction assay. REVEALS can also be incorporated into other custom pipelines to analyze complex behavior, such as MoSeq. In summary, REVEALS provides an interface for collecting behavioral data from one or multiple perspectives that, combined with deep learning algorithms, will allow the scientific community to discover and characterize complex behavioral phenotypes to understand brain function better.
Antisense Oligonucleotide Targeting Hepatic Serum Amyloid A Limits the Progression of Angiotensin II-Induced Abdominal Aortic Aneurysm Formation
Authors: Shridas Preetha , Ji Ailing , Trumbauer Andrea C , Noffsinger Victoria P , Meredith Luke W , de Beer Frederick C , Mullick Adam E , Webb Nancy R , Karounos Dennis G , Tannock Lisa R
Published: August 2023

Background and aim

Obesity increases the risk for abdominal aortic aneurysms (AAA) in humans and enhances angiotensin II (AngII)-induced AAA formation in C57BL/6 mice. We reported that deficiency of SAA significantly reduces AngII-induced inflammation and AAA in both hyperlipidemic apoE-deficient and obese C57BL/6 mice. The aim of this study is to investigate whether SAA plays a role in the progression of early AAA in obese C57BL/6 mice.

Methods

Male C57BL/6J mice were fed a high-fat diet (60% kcal as fat) throughout the study. After 4 months of diet, the mice were infused with AngII until the end of the study. Mice with at least a 25% increase in the luminal diameter of the abdominal aorta after 4 weeks of AngII infusion were stratified into 2 groups. The first group received a control antisense oligonucleotide (Ctr ASO), and the second group received ASO that suppresses SAA (SAA-ASO) until the end of the study.

Results

Plasma SAA levels were significantly reduced by the SAA ASO treatment. While mice that received the control ASO had continued aortic dilation throughout the AngII infusion periods, the mice that received SAA-ASO had a significant reduction in the progression of aortic dilation, which was associated with significant reductions in matrix metalloprotease activities, decreased macrophage infiltration and decreased elastin breaks in the abdominal aortas.

Conclusions

We demonstrate for the first time that suppression of SAA protects obese C57BL/6 mice from the progression of AngII-induced AAA. Suppression of SAA may be a therapeutic approach to limit AAA progression.
Stakeholder management challenges and strategies for sustainability issues in megaprojects: case studies from Australia
Authors: Senaratne Sepani , KC Abhishek , Rai Siryana
Published: August 2023

Purpose

Megaprojects are financially large and complex in scope, which require engagement of stakeholders from various institution and communities. With increased concerns from stakeholders on sustainability related issues, from environmental to socio-economic perspective, managing megaprojects has become quite challenging. Hence, there should be proactive approaches in active engagement of stakeholders from the start of the projects to overcome such issues. Currently, there is a knowledge gap on stakeholder management strategies specific to megaprojects on managing sustainability issues.

Design/methodology/approach

This research has adopted review of secondary data from case studies to identify stakeholder management challenges and strategies in megaprojects around Sydney area. The documents related to three different projects were reviewed and data were collected through qualitative content analysis and coding with use of NVivo software for within case analysis and was followed by thematic approach for cross case analysis.

Findings

Every case study project's sustainability-related stakeholder issues are more similar than different to others. Differences are mostly in terms of intensity of impact of any issue in a particular project, and/or intensity of impact at certain phase of any project. Moreover, significant sectors and strategies have been identified for key focus to manage environment and socioeconomic issues. Whatever be the strategies, in case of megaprojects, they need to be mostly proactive.

Originality/value

This research has extended the knowledge on stakeholder management, in relation to managing sustainability-related issues of megaprojects during their design, construction and operation phases. This research offers useful strategies for project teams of megaprojects to develop a proactive stakeholder management plan, addressing unavoidable sustainability challenges.
Learning and development at PTCL and advent of COVID-19
Authors: Soomro Mubeena , Memon Ubedullah , Ali Masroor , Qureshi Naveed Akhtar
Published: August 2023

Learning outcomes

1. Analyze the concept of disruptive change and its impact on organizational learning and development; 2. Develop the ability to identify and implement effective behavioral training interventions; 3. Understand the learning and development process; 4. Evaluate the challenges associated with online learning and explore strategies to overcome them; and 5. Recognize the significance of online learning in the current era and acquire knowledge and skills using online tools and applications for different job roles.

Case overview/synopsis

This case focuses on the new challenges that Shazia Zaheer, who is Head of the Learning and Development Department, is experiencing as a consequences of COVID-19 in her department. As her learning and development department has been focused primarily on traditional learning modes since the inception of Pakistan Telecommunication Limited (PTCL), she is facing additional challenges in adopting online learning because PTCL has undergone significant structural change. Since 1947, PTCL has been a state-owned enterprise. In 2005, the Pakistan Government privatized PTCL. This privatization resulted in numerous structural changes in management, hierarchy, chain of command, pay structure, product lines, technology and other factors. Employees were reduced from 90,000 to 23,000 as part of a volunteer separation plan, and a new scheme was introduced to streamline the process and improve efficiency. However, the employees at PTCL reacted to this transformation with union strikes and behavioral changes. Hence, this became a daunting challenge for Shazia Zaheer to change employees’ mindsets and instill corporate culture values. Nonetheless, she successfully won the half battle by changing the mindset of employees, and then she faced another challenge, COVID-19. This new normal brought new challenges for Shazia to implement online learning as her department relies solely on traditional modes of learning (classroom-based learning).

Complexity academic level

This case will be a good teaching aid if included in any courses on “Training and Development,” “Human Resource Management,” “Change Management” and “Online Learning” It would be better at the undergraduate (specialization courses) or graduate level.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 6: Human Resource Management.
The paradox of workplace flexibility: navigating through the case of Career Pandit
Authors: Datta Pallavi , Balasundaram Sathiyaseelan , Aranha Rekha Hitha , Chandran Vijaya
Published: August 2023

Learning outcomes

The learning objectives are intended to stimulate the students’ comprehension of the various challenges faced by Indian startups in the digital ecosystem. With the changing working dynamics in organizations around the globe, managers are expected to explore unconventional business models to facilitate operational growth. The case study is a valuable resource for graduate students to enhance and evolve their critical thinking and solution-oriented skills as forthcoming managers of digital businesses. Students should be able to analyze the case, respond to the questions and evaluate the consequences of workplace flexibility, moonlighting and its applicability in an organizational context. With the Indian Government introducing schemes such as the Digital India initiative and Startup India, it is predicted that numerous startups will opt for digital business standards and a remote work approach. The case bridges classroom theories and a real-life digital company to help students connect with emerging market scenarios.

Case overview/synopsis

During the digital era, India witnessed a shift in companies’ work culture, which amplified when COVID-19 hit the country. Organizations started to work remotely and experienced the numerous benefits it brought. The comfort of working from home was greater for digital businesses whose significant operations could be performed online. However, is it really that productive for digital companies to telecommute? The case illustrates how a digital company, Career Pandit, formed in 2018, unfurls and expands its business and further highlights the challenges the pandemic raised concerning people management. In addition to the discussion, the purpose of the case is to determine the implication of workplace flexibility and moonlighting and how Indian startups cope with the uncertain future challenges it brings.

Complexity academic level

Under graduate and postgraduate students.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 6: Human Resource Management.
Design-based research to develop lesson study for transformative assessment: teachers’ reactions, learning, organizational support, and use
Authors: Abate Melaku Takele , Wedajo Abbi Lemma , Hunde Adula Bekele
Published: August 2023

Purpose

This study aimed at exploring mathematics teachers’ reactions, learning, school leaders’ support, and the use of the lesson study for transformative assessment (LSforTA) program ideas in practice.

Design/methodology/approach

The LSforTA program was new and therefore, a local and grounded approach was needed to examine teachers’ knowledge and their skills acquired using LSforTA. A design-based research approach was therefore selected to evaluate and refine the LSforTA approach.

Findings

The program affected teachers’ practices of transformative assessment and enhanced their knowledge and skills in assessing students transformatively in a positive way. The paper concludes how LSforTA procedures were adapted in response to this evaluation and provides suggestions for future development and research.

Originality/value

With its original combination of conceptual and theoretical lenses, the research contributes to the academic literature by linking transformative assessment, lesson study and school context. This connection provides new opportunities for teachers to develop strategies to create meaningful assessment practices embedded with their instructional process in the context of their schools.