bluuebunny/crossref_metadata_2025_split huggingface dataset:
A systemic approach for evaluating biological function of acetyllysine in Danio rerio
Authors: Kim Sun Joo , Kwon Oh Kwang , Sung Eun Ji , Lee Sangkyu 
Published: November 2023

Zebrafish (Danio rerio) is a widely used vertebrate model in genetics and cell biology. Although studies in several mammalian species have been performed, the mechanism of lysine acetylation in D. rerio embryos is incompletely understood. Lysine acetylation is an important post‐translational modification. Since the development of mass spectrometry (MS)‐based proteomics technology, important roles of lysine acetylation beyond histones have focused on chromatin remodeling during the cell cycle and regulation of nuclear transport, metabolism, and translation. Here, we investigated the global acetylome in D. rerio embryos by using an MS‐based system. We identified 351 acetylated peptides and 377 non‐redundant acetylation sites on 189 lysine‐acetylated proteins in 5‐day post‐fertilization (hpf) embryos of D. rerio. Among lysine‐acetylated peptides, 40.2% indicated 3 motifs: (ac)KxxxK, (ac)KxxxxK, and Lx(ac)K. Of 190 acetylated proteins, 81 (42.6%) were mainly distributed in the cytoplasm. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that lysine acetylation in D. rerio was enriched in metabolic pathways. Additionally, 17 of 30 acetylated ribosomal proteins were evolutionarily conserved between zebrafish and humans. Our results indicate that acetyllysine might have regulatory effects on ribosomal proteins involved in protein biosynthesis.Support or Funding InformationThis work was supported by a National Research Foundation (NRF) grant funded by the Korean government (MSIP) (NRF‐2012R1A4A1028835 and ‐2014R1A1A2A16053716).
Optimized expression and purification of recombinant L‐asparaginase II: Tetramer stabilization by site‐specific covalent crosslinking of its subunits
Authors: Ramirez‐Paz Josell , Saxena Manoj , Griebenow Kai 
Published: November 2023

L‐Asparaginase II is a tetrameric periplasmic enzyme from E. coli, which plays a major role in the chemotherapy of acute lymphoblastic leukemia due to its great affinity (26 μM) toward asparagine catalyzing its hydrolysis. Proteolytic degradation is one of the main causes of its inactivation.1,2 Our purpose is to study how the covalent cross‐linking of asparaginase's subunits can affect its activity, stability and proteolytic susceptibility. To accomplish this, specific amino acids on the monomer's surface will be mutated to cysteine. The subunits can then be covalently linked through thioether chemistry using different lengths of maleimide‐functionalized polymers. So far, we have been able to produced recombinant L‐asparaginase II in high purity (>99% by SDS‐PAGE) and yield (15–20 mg/L & 50% recovery). We optimized the expression and purification of our system, to come out with a straightforward method consisting of fast‐concentration → desalting → anion exchange, which allows rapid production of the recombinant asparaginase (only 5 hours). Mass spectroscopy was employed to confirm the identity of the recombinant enzyme in mature form (without N‐terminal peptide). In addition, circular dichroism and fluorescence spectroscopy suggest an identical secondary and tertiary structure when compared to the natural asparaginase. The presence of the enzyme tetramer and monomer was demonstrated by native‐PAGE electrophoresis. Finally, the specific activity of the recombinant asparaginase was found to be equal to the natural enzyme, compared by two different methods.3,4 At this point, we tested the expression of the mutant (A38C‐T263C) that will allow for the specific linkage, and confirmed that it is secreted as active enzyme. Now we will proceed with the cross‐linking of the subunits and evaluate activity, stability and proteolytic susceptibility of the neo‐conjugate vs. the non‐conjugate asparaginase.Support or Funding Information(1) Research facilities at the UPR ‐ Chemistry Department, Facundo Bueso(2) Research facilities at the UPR‐Molecular Sciences Research Building3) RISE Program at the University of Puerto Rico ‐ Rio Piedras Campus
Targeting the Young Scientist Community through their Interest in Biochemistry and Molecular Biology
Authors: Oquendo Mabel Giselle Pérez , Lachapel Ivana Serrano , Soto Luis Haddock , Lugo Juan Ramírez 
Published: November 2023

The American Society for Biochemistry and Molecular Biology (ASBMB) Student Chapter at the University of Puerto Rico, Río Piedras (UPRRP), has as its primary focus to promote scientific interest in our students and the community. Given the growing need of researchers working on the many issues to be resolved in the field of Biochemistry and Molecular Biology, we want to genuinely inspire more people to get involved in this process to create and share knowledge. To inform about medical, technological and scientific advances, and encourage curiosity, and critical thinking, we performed journal clubs. However, to promote interaction between elementary, middle and high school students with university students who have scientific research experience, we accomplished community volunteer activities and outreach. As a result of our efforts in broadening scientific activities, our UPRRP chapter was awarded with ASBMB funds directed towards the organization of the “2nd Cellular and Molecular Biology Undergraduate Research meeting”. Through this symposium we achieved the participation of professors, graduate students, postdocs, and undergraduate students presenting local and summer research projects. Therefore, this meeting has been a platform for students interested in science, particularly in biochemistry and molecular biology area, are integrated into the scientific community. Conclusively, we aspire to build upon the foundations of the American Society for Biochemistry and Molecular Biology by serving as catalysts to inspire incoming students and everyone we may reach to contribute in our common pursuit of knowledge for the benefit of all.Support or Funding InformationRegional Meeting Award ‐ ASBMB
The Vitamin D Content of a High‐Fat Diet Modulates Brain Reward Neurochemistry
Authors: Kubant Ruslan , Chatterjee Diptendu , Pannia Emanuela , Anderson G. Harvey 
Published: November 2023

BackgroundObesity is associated with increased consumption and preference for palatable foods as well as reduced blood levels of 25[OH]D3, which has been linked to altered dopaminergic and serotonergic signalling in the brain. The effect of vitamin D on high fat diet induced changes in brain reward systems is unknown.ObjectiveTo determine if vitamin D plays a role in modulating hedonic regulation of food intake in the brain in response to chronic consumption of a high fat diet.Methods and DesignMale Wistar rats at 21 days of age were fed ad libitum for 14 weeks a high‐fat diet (60 kcal% fat) containing either: 1) the recommended amount (1,000 IU/kg diet) of vitamin D3 (HF‐RD) or 2) high vitamin D3 (HF‐HD, 7‐fold increase of the recommended amount). Rats fed a normal‐fat diet with the recommended amount of vitamin D3 (NF‐RD, 16 kcal% from fat) served as control. Body weight, food intake, serum 25[OH]D3, and concentrations of dopamine (DA), 3,4‐dihydroxyphenylacetic acid (DOPAC), serotonin (5‐HT), 5‐hydroxyindoleacetic acid (5‐HIAA) were measured in the nucleus accumbens (NAc) and β‐endorphin in the ventral tegmental area (VTA). DA and 5‐HT turnover rates were calculated by the ratio of their primary metabolites DOPAC to DA and 5‐HIAA to 5‐HT respectively, and used as an index of dopamine/serotonin transmission.ResultsThe HF‐RD group consumed more calories and gained more weight than the NF‐RD group as well as exhibited increased DA (48%, P<0.05), DOPAC (330%, P<0.05), dopamine turnover (195%, P<0.05), 5‐HT (85%, P<0.05), 5‐HIAA (51%, P<0.05), and lower serotonin turnover (16%, P<0.05) in NAc. VTA levels of β‐endorphin were lower (46%, P<0.05) in the HF‐RD group compared to the NF‐RD. Supplementation of a HF diet with high vitamin D3 for 14 weeks resulted in a 3‐fold increase (P<0.05) in serum 25[OH]D3 and reduction (≈30%, P<0.05) in DOPAC levels and dopamine turnover compared to the HF‐RD group, but had no statistically significant effect on food intake, body weight, 5‐HT, 5‐HIAA, serotonin turnover rate or β‐endorphin levels in the brain.ConclusionThe vitamin D content of a high‐fat diet modulates brain reward neurochemistry and may be a factor in neurotransmitter‐mediated regulation of the reward‐seeking behaviors.Support or Funding InformationCanadian Institute of Health Research, Institute of Nutrition, Metabolism and Diabetes (CIHR‐INMD), Reference MOP‐130286.
Supplementation of Viscum album L. (mistletoe) might have a favorable effect on aging‐related muscle loss: A randomized, double‐blind, placebo‐controlled study
Authors: Lim Nam Ju , Kim Joohee , Kim Ji Yeon , Kwon Oran 
Published: November 2023

Aging‐related muscle weak is associated with degenerative loss of skeletal muscle mass and function. The present study was investigated to test whether Viscum album L. var. coloratum Ohwi (Mistletoe) supplement can strengthen muscle mass and muscle strength in elderly subjects. A 12‐week, double‐blinded, randomized, parallel‐group, placebo‐controlled trial was performed in 63 subjects over 60 years of age (60–75y). Subjects were divided into three groups (n=21 for each group): placebo, low dose of mistletoe (1g/d) and high dose of mistletoe (2g/d). We evaluated muscle mass and function between the three groups over 12 weeks by measuring muscle mass [Body composition analysis (Inbody), and the cross‐sectional muscular area], muscle strength [Electromyogram(EMG), knee flexion‐extensor strength (Cybex) and grip strength], and short physical performance battery(SPPB) [usual gait speed, timed get‐up‐and‐go test and posturography]. The results showed that the percent of relative change in muscle mass was not significantly different between the groups after the intervention period. In muscle strength, the peak torque (Flexor, left, 120°) and the set total work (Flexor, left, 120°) of cybex increased significantly in high dose of mistletoe (P=0.017, P=0.002, respectively) compared to placebo group. In SPPB, the low dose of mistletoe was higher than other groups in changes of the 6‐minute gait speed (P=0.048). In conclusion, mistletoe was proven to beneficial role in muscle strength and function in older adults, regardless of its dose. In further study, the elucidation of molecular pathway which is associated with regulation of muscle biogenesis is needed to perform in biopsy muscle.Support or Funding InformationThis work was supported by the Ministry of Science, ICT & Future Planning (Bio‐synergy Research Project NRF2012M3A9C4048761) and BK21PLUS through the National Research Foundation.
24‐week exposure to dietary oxidized tyrosine (O‐Tyr) induces renal injury in rats through activation of p38 signaling
Authors: Li Zhuqing , Shi Yonghui , Le Guowei , Ding Yinyi , Zhao Qi , Tang Xue 
Published: November 2023

Oxidized tyrosine (O‐Tyr) products such as Dityrosine (Dityr) and 3‐nitrotyrosine (3‐NT) have been widely detected in many commercial protein products. Since dietary O‐Tyr has been demonstrated to induce health harmful effects in our previous study, the objective of the present study was to examine renal toxicity of dietary O‐Tyr, focusing on oxidative stress and fibrosis changes. Male Sprague‐Dawley (SD) rats were treated with 0, 2, 4 and 8 g O‐Tyr/kg diet each day for 24 weeks. A group of rats treated with 8 g Tyr/kg diet were set as Tyr control. The kidney index, urine volume (UV), serum creatinine (Scr), blood urea nitrogen (BUN) and oxidative stress indexes were tested to evaluate renal injury. Expression of extra cellular matrix (ECM) contents, including hyaluronic acid (HA), laminin (LN), procollagen type Icarboxy terminal peptide (ICTP) and type I procollagen peptide (PINP), together with Masson staining of kidney slices was tested to investigate renal fibrosis. mRNA and protein expression related to p38 pathway was detected using the method of quantitative real‐time reverse transcription PCR, western blot and immunohistochemical staining. Our results showed that 24‐week feeding of O‐Tyr elevated kidney index, UV, Scr and BUN levels. Renal oxidative stress was evidenced by increased levels of ROS, protein carbonyl (PC), Dityr, 3‐NT, advanced oxidative protein products (AOPPs), malondialdehyde (MDA) and decreased activities of glutathione peroxidase (GPX), superoxide dismutase (SOD) and catalase (CAT). The expression of transforming growth factor‐β (TGF‐β), tumor necrosis factor‐α (TNF‐α), interleukin‐1β (IL‐1β) and IL‐6 in the kidneys increased after O‐Tyr treatment, suggesting renal inflammation. O‐Tyr also distinctly increased the phosphorylation of p38, enhanced fibrosis‐related TGF‐β1 and Smad 2/3 expression. In addition, elevated ECM contents, including HA, LN, ICTP and PINP, accompanied with results of Masson staining also supported renal fibrosis changes. All these changes are dose‐dependent in O‐Tyr treated group. Overall, our results suggested that O‐Tyr induces renal oxidative stress and renal fibrosis, which may be mediated through the activation of p38 signaling.Support or Funding InformationThe present study was supported by the 12th Five‐Year Plan for for Science and Technology Development (No. 2012BAD33B05)
Exploratory Brain Metabolomics: Sudden Infant Death Syndrome
Authors: Garvey Sean M. , Aggarwal Vasudha , Lai Chron‐Si , Lieblein‐Boff Jacqueline C. , Kuchan Matthew J. 
Published: November 2023

Sudden Infant Death Syndrome (SIDS) is the sudden, unexplained passing of an infant during sleep within the first year of life. The diagnosis of SIDS is one of exclusion, with no plausible explanation following autopsy and investigation of the death scene. Most of our present understanding of SIDS comes from epidemiological studies, and much is less known about molecular etiology. One candidate mechanism is that abnormalities in brainstem biochemistry cause altered neural control of breathing, leading to rousing defect and apparent SIDS. The objective of this study was to identify novel brain biochemicals associated with SIDS. Postmortem human infant brain tissue specimens from 28 decedents underwent comprehensive metabolomic profiling (SIDS, n=15; non‐SIDS, n=13). A total of 87 brain specimens were collected from 4 different regions of the brain associated with learning and memory, including the auditory cortex (AC, n=11), frontal cortex (FC, n=27), hippocampus (HC, n=22), and occipital cortex (OC, n=27). The contributions of both SIDS status and age to differential abundance of biochemicals were determined using Wilcoxon rank sum and Spearman correlation tests. A total of 247 known biochemicals were detected. Between SIDS and non‐SIDS specimens, 2 biochemicals in the AC, 12 in the FC, 9 in the HC and 10 in the OC were detected at significantly different levels (p<0.05). The most striking metabolomic pattern in SIDS vs. non‐SIDS specimens was attributed to changes in the urea cycle. Urea levels were 34% and 45% lower in the OC and HC, respectively, from SIDS brains, suggesting hyperammonemia. Also related to urea cycle, SIDS specimens showed changes in spermidine (−29% in OC), citrulline (+94% in HC), aspartate (+49% in FC and +35% in HC), arginine (+17% in FC) and 4‐guanidobutanoate (+31% in HC), relative to non‐SIDS specimens. Carbohydrate metabolism was altered, as glucose, fructose and sorbitol levels trended downward in all 4 SIDS brain specimens. Changes in both fructose (−70% in OC) and sorbitol (−59% in FC) achieved significance. Protein metabolism was also altered. The tryptophan metabolite kynurenine and the valine metabolite α‐hydoxyisovalerate were 37% and 74% lower in SIDS OC, while cysteine (+2.1‐fold) and cysteine‐glutathione disulfide (+2.2‐fold) increased in SIDS FC. Pseudouridine was ~30% decreased in each of FC, HC and OC from SIDS brains, suggesting differences in tRNA metabolism. Additionally, correlation analysis of biochemical levels vs. age of infant showed remarkable differences between SIDS and non‐SIDS. For example, non‐SIDS HC and OC age correlated with 7 and 22 biochemicals, respectively, while SIDS HC and OC age correlated with 29 and 49 biochemicals. In sum, we have identified several new candidate brain biochemicals and pathways, such as the urea cycle, associated with SIDS.Support or Funding InformationFunding for this study was provided by Abbott Nutrition.
Neck circumference cut‐off values as prognostic variable of childhood overweight/obesity by sex and age
Authors: VARELA‐MOREIRAS GREGORIO , Sanchez‐Campayo Elena , Angulo‐Diaz‐Parreño Santiago , Avila José Manuel , Partearroyo Teresa 
Published: November 2023

BackgroundEarly detection of childhood obesity play a crucial role in the prevention of diseases during adulthood. At present, the most commonly used screanning tool for detecting overweight/obesity in children is the body mass index for age percentile, although this rate is not able to provide information on fat distribution. An emerging marker of obesity indicative of central body fat distribution is the neck circumference (NC). However, the neck cut‐off in relation to Spanish children suffering the overweight/obesity in Spanish children has not been well elucidated.ObjectiveThe aim of this study was to evaluate the potential differences between different diagnostic criteria at national and international level (Orbegozo Foundation (OF), IOTF and WHO) to define overweight and obesity in order to establish the optimal cut‐off values of NC in Spanish children aged 3 to 12, and finally to determine if the NC could serve as a variable prognosis of childhood obesity.MethodsThis school‐based cross‐sectional study was carried out during academic course 2014–15, surveyed schoolchildren aged 3 to 12 years old of both genders (n=2725), from the town Villanueva de la Cañada (Madrid, Spain) already included in the THAO‐Child Health program (Global EPODE).NC, waist circumference (WC), weight and height were measured according to the ISAK criteria. References used of the international cut‐offs to define overweight or obesity were the ones from the World Health Organization (WHO) and the International Obesity Task Force (IOTF), but also the national BMI cut‐offs from the Orbegozo Foundation (OF).Receiver operating characteristic (ROC) curves and area under the curve (AUC) were analyzed with Matlab (R2010a) software version 7.11 programmed by the group research.ResultsThe NC cut‐off points varied from 0.733 to 0.940, sensibility (50–100%), specificity (61–100%) according to IOTF criteria, from 0,666 to 0,950, sensibility (50–97%), specificity (64–100%) according to WHO criteria and from 0.438 to 1.000, sensibility (70–100%), specificity (43–100%) according to OF criteria.ConclusionThe Cut‐off points proposed in the present study between different diagnostics criteria at national and international level are the first reference data on Spanish Children's NC. These new references seem to be an alternative method more easy to manage and valid as criterion diagnosis of childhood overweight/obesity.
LIM Homeobox 2 (LHX2) is a Downstream Intermediate of FGF in the Induction of SHH Expression in the Developing Limb
Authors: Watson Billy A , Pira Charmaine U , Real Daniel M , LaBarba Dean J , Oberg Kerby C 
Published: November 2023

Limb development involves the integration of signaling events along three interconnected axes. Growth and patterning along the proximal‐distal and anterior‐posterior axes are directed by a positive feedback loop between Fibroblast growth factors (FGFs) and Sonic hedgehog. Loss of either morphogen leads to a reduction in the expression of the other. Thus, we hypothesize that downstream targets of FGF signaling act as intermediaries to regulate SHH expression in the developing limb bud.Overexpression of FGF in the posterior region of the developing limb bud results in ectopic SHH expression. DNA microarray analysis, following FGF bead application, revealed ~260 gene targets upregulated >1.5 fold. One target, LHX2 (LIM Homeobox 2), encodes a transcription factor that is highly conserved across species, is expressed in the distal limb mesenchyme, and implicated in the integration of signaling inputs from the apical ectodermal ridge ‐ FGFs, zone of polarizing activity ‐ SHH, and the dorsal ectoderm ‐ WNT7a. Furthermore, LHX2/LHX9 double knockout mice show a marked reduction in SHH expression, confirming a role for LHX2 in regulating the signals that direct limb patterning and growth.Our results indicate that LHX2 is a primary response target of FGF signaling and participates in the induction of SHH expression, but LHX2 overexpression alone is not sufficient to induce SHH. LHX2 overexpression in the presence of an FGF bead results in enhanced ectopic SHH expression suggesting that FGF signaling also induces a protein partner necessary for the LHX2‐modulation of SHH expression. This finding is consistent with the fact that the LIM homeodomain transcription factor family generally requires a protein partner to elicit its effects. We therefore propose that LHX2 is a necessary collaborative intermediate in the FGF‐to‐SHH pathway.
Study of the Genesis of Persistent Fetal Vasculature through Clinical Observations of Two Pediatric Patients
Authors: Dong BaiXia , Wang Long , Hong Ying , Chen Huijin , Ma Zhizhong 
Published: November 2023

PurposePersistent fetal vasculature (PFV) is a rare congenital disease caused by fetal blood vessels remaining in the eyes, with various residues and persistent hyperplasia. A series of observations in 2 typical PFV were conducted to better understand fatal development in normal eyes and to illustrate involved controversies.MethodsCase One was an 11‐month girl who was found to have leukocoria accompanied by black spherical goiter in the right eye approximately 50 days after birth. Case Two was a 3‐year old girl who was found to have leukokoria at birth. IN both cases, image data prior to surgery and series of photographs during the procedures were carefully colliaected and reviewed comparatively with surgical video record. Novel tissue samples obtained from surgeries were observed histopathologically. Comprehensive analysis was carried out with literature review,ResultsMajority of the abnormal signs were concomitant with those that Goldberg described in Jackson Memorial Lecture emphasizing the congenital anomalies caused by different degrees of PFV, which seemingly existed in isolation, but were intrinsically syntrophic. Pigment epithelium layer of iris detoured over stoma through pupil to adhere with the back surface of cornea, which manifested as an iris cyst. Trace of fatal development supplied a hard evidence that corneal endothelium was originated from neuroectodermal cells. Network profile of persistent papillary membrane tended to be formed by anterior tunica vasculosa lentis while the remnants were coated by iris stromal tissues which were believed to be originated from neural crest cells.ConclusionsClose relation between corneal endothelium and pigment epithelium of iris at early stage of fatal development was evidenced by clinical observations in the two pediatric cases. Corneal endothelium and Descemet's membrane were most possibly originated from neuroectodermal and spread with the manner migrated from centre to periphery. Neural crest cells went forward to center from periphery via the staggered gap between developing endothelium and anterior surface of optic cup to form stroma of iris. Mechanism of persistent pupil membrane formation could be a result of mutualism between anterior tunica vasculosa lentis and stroma of iris.