bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of neuroanatomy on my career: from adult neurogenesis to in vitro disease modelling
Authors: Merkle Florian 
Published: November 2023

I am truly honored to be selected for this year's Young Investigator Award. It only seems appropriate to highlight how insights from neuroanatomy have shaped my career. I have always marvelled at how something as fantastically complex and beautiful as the brain could develop, so I pursued this curiosity by studying adult neurogenesis as a PhD student. By observing and taking advantage of the unique anatomical characteristics of early stem cells, my colleagues in Arturo Alvarez‐Buylla's laboratory and I demonstrated the lineage relationship of embryonic and adult neural stem cells. We further labelled stem cells in different regions of the adult neurogenic niche to show that they are better classified as distinct and restricted progenitors than homogeneous multipotent stem cells, and in the process identified four novel types of adult‐born interneurons. As a postdoctoral fellow, I used insights from developmental biology and anatomy to develop a method to differentiate human pluripotent stem cells into specific populations of hypothalamic neurons that regulate essential behavioral and physiological functions, such as feeding and sleep. In my own laboratory, we are now using single cell RNA sequencing and cellular assays to explore the functional heterogeneity of in vitro‐derived neurons. We then use these insights to map neuronal sub‐populations back to the mouse and human brain, where their anatomical location provides essential clues as to their likely function in the organism. Although new tools and evolving research interests have altered the trajectory of my career, neuroanatomy has provided a constant link.Support or Funding InformationThe research presented in this talk was supported by the National Science Foundation, the National Institutes of Health, the Jane Coffin Childs Memorial Fund for Cancer Research, the Harvard Stem Cell Institute, and the Howard Hughes Medical Institute. Current funding sources include the Wellcome Trust, the Medical Research Council, the Academy of Medical Sciences, and the University of Cambridge.
Promising effects of laser therapy and the natural latex protein on sciatic nerve crushed. Ultrastructural, sensory and functional study
Authors: Dias Fernando Jose , Simões Ana Leda Bertoncini , de Cássia Carmo Elisabete , Cury Diego Pulzatto , Almeida Sonia Regina Yokomizo , Dias Paula Elisa , Fazan Valeria Paula Sassoli 
Published: November 2023

Treatment of lesions that affect peripheral nerves still presents a challenge, in this context the low‐level laser (LLL) and the protein of the natural latex (Hevea brasiliensis, F1) showed positive effects.The aim of this study was to analyze the effects of LLL associated with F1 in crush injuries of the sciatic nerve (15 kgf, 10') in rats. Six groups (n=24) of rats (♂, 250 g): C ‐ Control; E ‐ Exposed nerve without crushing; Le ‐ injured nerve without treatment; L ‐ injured nerve LLL irradiation (15 J/cm2, 780 nm); F1 ‐ injured nerve with application of F1 protein (0.1%); and LF1 ‐ injured nerve with the F1 protein and LLL irradiation. After 1, 7, 14, 28, 56 and 180 days of nerve injury of sensory and functional analyzes were performed: 1. mechanical allodynia (von Frey); 2. Pressure testing the paw (Forceps); 3. Grip strength test and 4. Motor function (SFI). After 3, 15, 57 and 181 days of nerve injury, the animals of each subgroup (n=6) submitted to intracardiac perfusion (2.5% glutaraldehyde in cacodylate buffer 0.1 M, pH 7.2), the sciatic nerve samples were collected and processed to ultrastructural analysis.The results revealed that the controlled nerve compression (15 kgf) was intense, thus spontaneous recovery was not enough to restore the normal characteristics of the sciatic nerve allowing to evaluate the effects of proposed therapies. The three treatment protocols proposed LLL, F1 and LLL+F1 revealed improvements in ultrastructural characteristics when compared with the untreated injured animals. It was noted correlation between these data and those functional sensory and motor, which also showed improvements with the treatments applied. All treatments applied resulted in improvements in the characteristics and tests evaluated, the time in all cases was an important factor in this recovery however in some functional tests there was an acceleration of improvements, and the animals that received F1 associated or not to LLL had generally the best results.Support or Funding InformationFunding: FAPESP 2014/07253‐4
Unraveling gene regulatory mechanisms in meiotic differentiation
Authors: Brar Gloria , Cheng Ze , Van Dalfsen Kelsey , Eisenberg Amy , Hollerer Ina 
Published: November 2023

Meiosis is a well‐conserved program of cellular differentiation. We performed genome‐wide measurements of translation using ribosome profiling through meiosis in budding yeast to better understand the molecular basis for the full cellular restructuring that accompanies meiotic chromosome segregation. This first global glimpse at translation through a developmental process revealed great complexity to the protein complement of these differentiating cells, both in the number and the structure of expressed genes. Nearly every gene in the yeast genome was translated in meiotic cells in a strongly stage‐specific manner, including thousands of genes with no previously known meiotic role. Prominent among these was key regulators of conserved stress response pathways, suggesting that meiotic cells coopt such pathways for programmed cellular remodeling. Translational regulation contributed broadly to the timing and levels of protein synthesis through several disparate and complex mechanisms, including use of upstream Open Reading Frames Additionally, meiotic translation of thousands of novel short ORFs was observed, including on transcripts previously thought to be noncoding and as alternate translation products from characterized transcripts, expanding our view of what constitutes a coding region even in the most well annotated eukaryotic genome.Support or Funding InformationI am grateful for the NIH funding (DP2‐GM119138 and P50‐GM102706) that currently supports research in my lab, along with investigator awards from the March of Dimes, Alfred P. Sloan Foundation, and Pew Charitable Trusts.
Ultrafast recycling of synaptic vesicles
Authors: Watanabe Shigeki 
Published: November 2023

Neurons can fire at extremely high rates. To sustain neurotransmission, synaptic vesicles must be recycled locally at synapses. Two models for synaptic vesicle endocytosis have been put forward based on the morphological studies in frog neuromuscular junctions. Heuser and Reese proposed that endocytosis occurs via a slow mechanism using clathrin scaffolds. Ceccarelli and his coworkers proposed a fast mechanism, kiss‐and‐run. Since then, many studies have sought to identify the mechanism for synaptic vesicle endocytosis. However, instead of resolving the issue, conflicting evidence has accumulated over the years. The molecular studies have suggested clathrin and clathrin‐associated proteins are essential. However, the kinetics studies have suggested that both forms co‐exist. Our data identify a third pathway that is fast, but requires clathrin to regenerate vesicles.To investigate how endocytosis takes place, we developed a method, ‘flash‐and‐freeze’ that couples optogenetic stimulation with rapid high‐pressure freezing and captures endocytosis at millisecond temporal resolution. To our surprise, vesicle membrane is recovered via ultrafast endocytosis within 100 ms following a single stimulus. The large endocytic vesicles then fuse to form an endosome and are resolved by clathrin into synaptic vesicles in 5–6 s. When experiments are performed at 20°C instead of 37°C, ultrafast endocytosis fails, and clathrin regenerates synaptic vesicles directly from plasma membrane. These results suggest that recycling of synaptic vesicles is normally a rapid two‐step process: ultrafast endocytosis that removes excess membrane from the surface and then clathrin‐mediated biogenesis of synaptic vesicles from endosomes.Support or Funding InformationSW is supported by JHU startup fund and JHU discovery fund.
Malaria derived extracellular vesicles influence human neutrophils function
Authors: Babatunde Kehinde Adebayo , Walch Michael , Fellay Isabelle , Kharoubi‐Hess Solange , Filgueira Luis , Ghiran Ionita , Mantel Pierre‐Yves 
Published: November 2023

IntroductionA dysfunctional innate immune response is believed to provide immune evasion of the malaria parasites, but also to cause increased susceptibility to bacterial infections. Neutrophils are the most abundant cells found in the blood circulation in direct contact with parasite infected red blood cells (iRBCs). However neutrophils population with reduced oxidative burst activities are present during malaria infection. These observations suggest that neutrophil responses are fundamentally defective in malaria patients. Extracellular vesicles (EVs) are iRBCs derived vesicles and contain both parasite and host materials, including microRNAs. In this present work we investigated, how EVs modulate neutrophil response.ResultsInterestingly, we have reported that malaria EVs contain miR451a, a miRNA that is known to regulate neutrophil activity. We have also monitored the uptake of EVs by neutrophils by fluorescence microscopy and real‐time polymerase chain reaction techniques. To address the role of miR451, we investigated the influence of malaria‐induced EVs on human neutrophil functions in vitro and the effect of miR451a on the transcriptional response in differentiated HL‐60 cells to bacterial infections. We demonstrated that EVs inhibit neutrophil function by inhibiting neutrophils ability to produce ROS and suppression of cytokine secretion. The neutrophils were also affected in their bactericidal activity.ConclusionOur data indicate that malaria EVs deliver miR‐451 into neutrophils to interfere with their capacity to kill bacteria. We describe a new mechanism of cellular communication between parasites and the host immune system. While EVs might increase tolerance to the parasites, they dramatically affect the resistance to a co‐infection by bacteria. The elucidation of the immune regulatory role of EVs might lead to the development of new diagnostic tools and therapies.
Phosphoinositide conversion in the endolysosomal system
Authors: Haucke Volker , Ketel Katharina , Wallroth Alexander , Marat Andrea L , Lo Wen‐Ting , Schultz Carsten 
Published: November 2023

Phosphoinositides (PIs) form a minor class of phospholipids with crucial functions in cell physiology, ranging from cell signalling and motility to a role as signposts of compartmental membrane identity. Phosphatidylinositol 3‐phosphates are present at the plasma membrane and within the endolysosomal system, where they serve as key regulators of both cell signalling and of intracellular membrane traffic. In my talk I will cover our recent advances in the analysis of the metabolic pathways that regulate cellular synthesis of PI 3‐phosphates at distinct intracellular sites and discuss the mechanisms by which these lipids regulate cell signalling and membrane traffic. Finally, I will provide a framework for how PI 3‐phosphate metabolism is integrated into the cellular network.Support or Funding InformationDeutsche Forschungsgemeinschaft (DFG), TRR186, SFB740
Mechanisms of Zinc Metallostasis in Bacterial Pathogens
Authors: Giedroc David , Capdevila Daiana A. , Martin Julia E. , Edmonds Katherine A. , Wu Hongwei 
Published: November 2023

First‐row late d‐block transition metals from Mn to Zn play critical and distinct roles in many aspects of cellular metabolism. In bacterial pathogens, metalloregulation of transcription underscores physiological adaptation to host‐mediated transition metal starvation and toxicity, required to maintain metal homeostasis. In zinc (Zn) homeostasis, a pair of metal‐sensing transcriptional repressors regulate the transcription of metal uptake and efflux transporters, where Zn typically allosterically activates or inhibits, respectively, DNA operator‐promoter binding. We have interests in the molecular underpinnings of allostery in metalloregulatory proteins, transition metal transporter function and the impact that dysregulation of the process has on cellular physiology. In the model Gram‐positive respiratory pathogen, Streptococcus pneumoniae, the Zn uptake regulator is the multiple antibiotic resistance repressor (MarR)‐family protein, adhesin‐competence repressor (AdcR), while the efflux regulator is a novel tetracycline repressor (TetR) family protein, streptococcal zinc activator (SczA). These are interesting regulatory targets with which to probe allosteric regulation of DNA binding by metals since in the vast majority of MarR and TetR repressors, the regulatory ligand functions as an allosteric inhibitor of DNA binding (+ΔGc); in both AdcR and SczA, the sign on the allosteric coupling free energy, ΔGc, is negative or favorable. NMR solution structural studies of both backbone and methyl side‐chain flexibility as a function of allosteric state in AdcR will be discussed, as will NMR studies of AdcR‐regulated Zn uptake transporter, and the Zn efflux regulator SczA. In addition, recent findings of effect of host‐imposed Zn toxicity on pneumococcal physiology will also be presented.Support or Funding InformationSupported by the US National Institutes of Health grant GM118157.
Substrate Conformational Dynamics in Proteolysis
Authors: Radisky Evette S. 
Published: November 2023

Enzyme catalytic power and specificity derive from dynamic interactions between enzymes and their substrates. While considerable effort has been devoted to understanding how enzyme conformational dynamics can affect catalysis, the importance of conformational dynamics within protein substrates has been overlooked. Proteases are ubiquitous enzymes that catalyze the hydrolysis of peptide bonds within protein substrates; they have served as key model enzymes for studying the molecular basis for catalysis and specificity. Recent work from our research group, focusing on trypsins and chymotrypsins as model proteolytic enzymes, reveals that differing conformational dynamics in otherwise similar protein substrates can profoundly impact proteolysis. In this talk, I will present some of our recent findings, integrating evidence from crystal structures, molecular dynamics simulations, and enzyme kinetics studies, which implicate flexibility and conformational motions of protease substrates as critical determinants of proteolysis. Our studies suggest that specific substrate conformational dynamics have evolved to regulate biological proteolytic events. More generally, our work suggests that we must look beyond enzymes, and examine substrates also, to fully appreciate the importance of protein dynamics in enzyme catalysis.Support or Funding InformationSupported by NIH grant R01CA154387.
Mechanism and Regulation of RNA Polymerase II
Authors: Kaplan Craig D. 
Published: November 2023

Regulated gene expression by RNA Polymerase II (Pol II) is essential for organismal function and underpins development and response to environment in eukaryotes. Alteration to Pol II catalytic activity causes all aspects of transcription from initiation to elongation, termination, and RNA processing to be altered. We have undertaken high‐throughput genetic analyses to dissect the Saccharomyces cerevisiae Pol II active site and determine how individual residues of a critical Pol II domain – the trigger loop (TL) – function. These studies allow us to test models for Pol II function and illuminate the contributions of residues to basic Pol II functions. We have also characterized the mechanisms by which the small molecule thiolutin, a long known transcription inhibitor lacking defined mechanism, alters transcription and yeast cellular physiology. We show that while thiolutin has many in vivo effects, it directly inhibits Pol II activity in multiple ways, and thiolutin‐inhibited Pol II has unique properties not observed for another Pol II inhibitor, alpha‐amanitin. We will discuss how these and other studies allow us to learn about fundamental transcription mechanisms.Support or Funding InformationNIH GM097260, GM120450Welch Foundation A‐1763
Combined metabolomic and fluxomic assays suggest the existence of multiple pools of glucose‐6‐phosphate in perfused muscle
Authors: Previs Stephen , Herath Kithsiri , Petrov Aleksandr , Castro‐Perez Jose 
Published: November 2023

Glucose uptake and utilization (e.g. deposition in glycogen vs oxidation to CO2) by skeletal muscle represents a critical step to ensuring normal metabolic homeostasis. The ability to modulate glucose flux in muscle is of interest since it may affect better glucose control in subjects with impaired insulin action and/or overt diabetes. We initiated studies that used isolated perfused rat hindlimb as a model system in order to identify molecules that could alter glucose uptake and utilization, metabolomic and fluxomic analyses were used to track the fate of glucose molecules. Typical studies relied on 30–60 min open circuit perfusions, soleus and gastrocnemius were then dissected and freeze clamped. Samples were processed using standard homogenization steps and subjected to LC‐MS analyses. The data suggest greater uptake of 2‐deoxyglucose in soleus vs gastrocnemius under baseline conditions. The incorporation of [13C]glucose was then followed into glucose‐6‐ and glycerol‐3‐phosphate, lactate and several TCA cycle intermediates. The observed [13C]labeling patterns clearly demonstrate the generation of [13C]lactate but suggest minimal conversion of [13C]glucose to [13C]TCA cycle intermediates. Parallel labeling studies with [13C]acetate demonstrate [13C]labeling in the TCA intermediates, implying that mitochondria are active in the resting perfused muscle but that the muscle does not completely oxidize glucose. A striking observation however centers on a discrepancy between the enrichments of glucose‐6‐ vs glycerol‐3‐phosphate, the latter being much higher than the former (consistent in both muscles). The discrepancy in the [13C]labeling patterns can be explained by the existence of multiple pools of glucose‐6‐phosphate. These observations agree with previously reported data in hepatocytes and have important implications if/when one aims to use concentration profiles to infer aspects of metabolic control. For example, concentrations of glucose‐6‐phosphate are believed to play a central role in effecting glucose uptake (e.g. feedback inhibition). However, the existence of multiple pools complicates interpretations when one aims to link a change in metabolite concentration to a change in metabolic flux. We believe that one can use tracers to estimate overall flux rates but one should exercise caution when using concentration profiles to explain metabolic control points and therein identify reactions that are targeted by pharmacological manipulations.Support or Funding InformationAll authors were employed by Merck during the completion of these studies.
Watermelon and L‐Arginine Consumption Regulate Gene Expression Related to Serum Lipid Profile, Inflammation, and Oxidative Stress in Rats Fed an Atherogenic Diet
Authors: Beidler Joshua , Hooshmand Shirin , Kern Mark , Figueroa Arturo , Hong Mee Young 
Published: November 2023

Watermelon (Citrullus lanatus) is rich in L‐citrulline, a precursor of L‐arginine that may reduce cardiovascular disease (CVD) risk. The purpose of this study was to investigate the effects of watermelon powder and L‐arginine supplementation on lipid profiles, antioxidant capacity, and inflammation in rats fed an atherogenic diet. We hypothesized that watermelon and L‐arginine would increase antioxidant capacity and reduce blood lipids and inflammation by modulating hepatic expression of key genes. Three‐week‐old male‐weanling Sprague‐Dawley rats (total N = 32) were assigned to 3 groups and fed diets containing watermelon powder (0.5% wt/wt; n = 11), L‐arginine (0.3% as 0.36% L‐arginine HCl wt/wt; n = 11), or a control diet (n = 10) for 9 weeks. Food and water intake, body weight, and epididymal fat mass did not differ among the 3 groups of rats. However, watermelon and L‐arginine supplementation exhibited lower serum concentrations of triglycerides, total cholesterol, and low density lipoprotein cholesterol compared to control (P< .05). There were no significant differences for high‐density lipoprotein cholesterol. The watermelon and L‐arginine groups had significantly lower serum levels of C‐reactive protein than the control group (P< .05). Superoxide dismutase, glutathione S‐transferase, and total antioxidant capacity were higher in the watermelon and L‐arginine groups compared with controls (P< .05). Activities of catalase, glutathione peroxidase, and glutathione reductase were not significantly different. Compared with rats consuming the control diet, rats consuming watermelon and L‐arginine exhibited significant upregulation of endothelial nitric oxide synthase (P< .05) and significant downregulation of fatty acid synthase, 3‐hydroxy‐3‐methyl‐glutaryl‐CoA reductase, sterol regulatory element‐binding protein 1, sterol regulatory element‐binding protein 2, cyclooxygenase‐2, and nuclear factor NF‐kappa‐B p65 (P< .05). There were no significant differences in expression of inducible nitric oxide synthase. In conclusion, these results support the hypothesis that watermelon improves CVD risk factors including lipid profile, oxidative stress, and inflammation by altering hepatic gene expression in a manner similar to L‐arginine supplementation.Support or Funding InformationThe study was funded by the US National Watermelon Promotion Board and the Kasch‐Boyer Endowed Scholarship in Exercise and Nutritional Sciences in San Diego State University.