bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accessory Quadrate of Liver & its Implications
Authors: Chandrasekaran Chithambaram 
Published: November 2023

IntroductionThe liver is the largest wedge‐shaped gland in the human body. Anatomically it is divided into right lobe and left lobes with quadrate & caudate lobes. The congenital abnormalities of human liver are rare and these are rarer than almost any other organs of the body. Various congenital abnormalities of the liver as agenesis of its lobes, absence of its segments, deformed lobes, decrease in size of lobes, lobar atrophy, hypoplastic lobes, and transposition of the gall bladder, extra caudate lobe and Riedel's lobe have been reported by various researchers. The quadrate lobe is an area of the liver situated on the under surface of the right lobe, bounded in front by the anterior margin of the liver; behind by the porta hepatis; on the right, by the fossa for the gall‐bladder; and on the left, by the fossa for the umbilical vein. It is oblong in shape, its antero‐posterior diameter being greater than its transverse.Methodology & ResultsAccessory quadrate lobe has been observed towards the left end of quadrate lobe, beside ligamentum teres in our routine dissections. Its shape was Triangular in shape with its dimensions of length – 3.4 cm from its apex to base, thickness 0.9 cm, base – 1.8 cm.ConclusionThese developmental anomalies of liver may cause confusion to clinicians during procedures like biopsy, transplantation, and lobectomies. So finding of this new variant under unique configuration of this lobe assumes more importance to anatomists including morphologists, and its knowledge may be of immense use to clinicians in the diagnosis and management of hepatic diseases and to embryologists for new developmental defect. Therefore, it is worth reporting as a new variant.Support or Funding InformationAMERICAN ASSOCIATION OF ANATOMIST(AAA)
Prevalence of the Anterolateral Ligament
Authors: Hinkley Jacob , Lampert Peter , Canby Craig 
Published: November 2023

First described by Paul Segond in 1879, the anterolateral ligament (ALL), is a fibrous band of tissue attaching to the distal aspect of the lateral femoral epicondyle and the proximal tibia just lateral to Gerdy's tubercle of the tibia. A previous study by Claes et al (2013) investigated the ALL and suggested that it had a prevalence of 97% in 41 unpaired cadaveric specimens. This study was designed to screen body donors to see if the ALL was as prevalent as previously reported. Forty‐six paired cadaveric knees were dissected from student gross anatomy courses. Of the 46, we were able to confidently examine 41 as the other five were excluded from the study either due to desiccation, knee transection, or knee arthroplasty. Our study found a prevalence of the ALL to be 51%, with males having greater prevalence than females (60% occurrence in males and 29% occurrence in females). Twenty of the body donors were found to have bilaterally distinct ALLs and one had a unilateral presence. Our study also found two different attachment sites on the distal femur possibly suggesting the ALL could be an independent structure and not just a projection of the lateral collateral ligament. Our study supports the existence of the ALL as a distinct structural entity albeit at prevalence less than previously reported.Support or Funding InformationSupported by the Anatomy Department, Des Moines University
PENO‐SCROTAL RAPHE ABSENCE & ITS HERNIATION
Authors: DOKIPARTY KRUPA DANIEL 
Published: November 2023

IntroductionThe scrotum is an anatomical male reproductive structure that consists of a suspended sack of skin and smooth muscle that is dual‐chambered located under the penis. One testis is typically lower than the other, which functions to avoid compression in the event of impact. The scrotum contains the external spermatic fascia, testes, epididymis, ductus deferens. It is a distention of the perineum and carries some abdominal tissues into its cavity including the testicular artery, testicular vein and pampinform plexus. A central cordlike line running over the scrotum from the anus to the root of the penis, marking the position of the scrotal septum.(Image‐1)MethodsIn our regular dissection course we found with an peculiar absence of penoscrotal raphe which has appeared as an single chambered scrotum with unified penis as absence of left corpora cavernosa & only presence of right corpora cavernosa and corpus spongiosum. The single chambered scrotum which was been herniated with the coils of intestines especially with terminal ileum & appendix with its omenta also peculiarly found with the absence of left side testis & its spermatic cord. (Imgaes ‐ 2,3,4,5)Conclusion
Complete absence of left side testis & its spermatic cord.
Single chambered scrotum with right testis only & herniated content.
Absence of median raphe.
Inguinal herniation should occur on right side but looping over towards the left side scrotal sac with the terminal ileum, vermiform appendix and its mesentry. (Images ‐ 6,7)
SignificanceSurgical correction is necessitate for this type of herniation. Surgery is the primary treatment for herniation. It's a very common operation and a highly successful procedure done by (“open” repair) or laparoscopic surgery (done through a small scope).Support or Funding InformationAMERICAN ASSOCIATION OF ANATOMISTS (AAA)
Transcription by the telomeric shelterin protein TRF2 is telomere‐length dependent ‐telomeric partitioning and global transcription
Authors: Chowdhury Shantanu 
Published: November 2023

Our data demonstrate TRF2 occupancy at the p21, as well as other promoters tens of Mb away from telomeres, to be dependent on telomere length. Of particular interest was the finding that p21 activation, following DNA damage, was transcriptionally regulated by TRF2 in a telomere‐length dependent fashion. Earlier studies have reported transcription to be telomere‐dependent in regions close to telomeres (subtelomeric) through primarily epigenetic mechanisms known as telomere‐positioning‐effect or TPE, which is unlikely to explain telomere‐dependent transcription tens of Mb from telomeres. Our results suggest a novel model of telomere‐dependent gene transcription involving telomere length in partitioning interstitial TRF2 binding.Support or Funding InformationWellcome Trust ‐ Department of Biotechnology India Alliance and Council of Scientific and Industrial Research
Specificity and Activity of DNA Polymerase DinB and Polκ Loop Swap Variants
Authors: Packer Morgan Renee , Antczak Nicole , Beuning Penny 
Published: November 2023

DNA damage is ubiquitous, arising from both natural and artificial sources. The presence of damaged bases in DNA requires the use of specialized Y‐family DNA polymerases, which have the ability to catalyze the insertion of a nucleotide opposite a damaged base and to continue elongation past this DNA lesion. This process of DNA replication past damaged nucleotide(s) is known as translesion synthesis. A major question is how different Y‐family DNA polymerases achieve specificity for different types of DNA damage. Previous work showed that the minor groove N2‐furfuryl‐deoxyguanosine lesion is the cognate lesion for both E. coli DinB and its human ortholog Polκ and that both DinB and Polκ are inhibited by bulky major groove lesions. It was further determined that the DinB loop1 R35A mutation enables the protein to bypass the non‐cognate N6‐furfuryl‐deoxyadenosine major groove lesion (Walsh, et al. 2013 DNA Repair 12:713). Our research probes the contributions of the loop1 region to the specificity and activity of DinB and Polκ, which is being assessed via the analysis of several loop swap variants that represent step‐wise progressive changes from the native loop1 to that of DinB, Polκ, or Dpo4. Dpo4 is of interest as it is a relatively non‐specific Y‐family polymerase. We show that DinB and Polκ have high specificity for their cognate lesion, and Polκ variants containing the DinB loop1 sequence retain activity similar to wild‐type Polκ, whereas the DinB variants do not. Thus, Polκ is more resistant to changes in its amino acid sequence.Support or Funding InformationThis work was funded by a National Science Foundation Research Experience for Undergraduates grant and the Department of Chemistry and Chemical Biology at Northeastern University.
Investigating the mechanism of trans‐lesion synthesis by Human DNA Polymerase Kappa
Authors: Younger Zane William , Allen Taylor , Benitez Benedetta Sampoli 
Published: November 2023

Our DNA is constantly under attack by both exogenous and endogenous chemicals that have the ability to damage it. If not repaired, these DNA adducts can lead to mutations to the DNA or even worse, they can halt replication, eventually leading to aging and/or cancer. Human DNA polymerase kappa (pol k) is a member of the Y‐family of DNA polymerases, known for their ability to conduct translesion synthesis of damaged DNA. Translesion synthesis allows for continued replication past lesions in the DNA that would otherwise stall or halt replication, leading to cell apoptosis. So far, the mechanism for lesion bypass discrimination by pol k is unclear. Recent studies suggested that similar to other polymerases, pol k might cycle between different open and closed conformations upon binding to DNA. Starting with one of the available crystal structures of pol k, we prepared eight different DNA/protein models and we solvated them in an octahedral water box with counter‐ions to a final ionic strength of 150 MM, using CHARMMgui. Subsequently, through molecular dynamics simulations, we tested the validity of the conformational change hypothesis by comparing the structural changes undergone by pol k in the presence of different templating lesions and with correct and incorrect incoming nucleotide. All simulations were performed using the program NAMD and were run for 10 ns each. We ran multiple simulations for the same system to ensure reproducibility of the results. Simulation of the binary system (just the protein and DNA without the incoming nucleotide) was also performed as a control system. By analyzing these different structures, we ascertained the residues crucial for fidelity and proposed a mechanism for lesion discrimination.Support or Funding InformationThis work was supported in part by a grant from the Rose M. Badgeley Residuary Charitable Trust.
The Critical Role of MAF1 in Repression of RNA Polymerase III Impacts Metabolic Efficiency in Mice
Authors: Willis Ian M , Bonhoure Nicolas , Moir Robyn D , Byrnes Ashlee , Hodroj Wassim , Praz Viviane , Preitner Frederic , Marcelin Genevieve , Chua Streamson , Martinez‐Lopez Nuria , Singh Rajat , Auwerx Johan , Willemin Gilles , Shah Hardik , Hartil Kirsten , Vaitheesvaran Bhavapriya , Kurland Irwin , Hernandez Nouria 
Published: November 2023

MAF1 functions to promote metabolic economy by repressing RNA polymerase (pol) III transcription of highly abundant cellular RNAs, most notably tRNAs, under conditions of nutrient limitation and cellular stress. This function of MAF1, along with its phosphoregulation in response to TOR kinase activity and its interactions with the RNA pol III transcription machinery, is conserved from yeast to humans. In addition to its effect on RNA pol III, the mammalian MAF1 protein has been shown to repress several genes transcribed by RNA pol II. However, the scope of MAF1 in repressing transcription at the genome level is not well defined in mammalian systems and studies on the impact of ablating MAF1 in metazoans have only just begun. To address these questions, we generated a whole body Maf1 knockout (KO) mouse. Maf1 KO mice are unconditionally viable and demonstrate a striking resistance to diet‐induced obesity and non‐alcoholic fatty liver disease. These phenotypes result from reduced food intake and increased metabolic inefficiency. Gene expression profiling of adipose tissue indicates that the pol II transcriptome is not significantly affected and together with other experiments, show that the increased energy expenditure of Maf1 KO mice does not result from induction of adaptive thermogenesis. Instead the data indicate that the obesity resistance of Maf1 KO mice is achieved by novel mechanisms of energy expenditure. These include the increased synthesis and turnover (futile cycling) of tRNAs in the whole animal and increased futile cycling of hepatic lipids. Metabolism in Maf1 KO mice is altered to meet the increased demand for metabolic energy: Lipolysis is increased in eWAT; polyamine synthesis is affected in liver and skeletal muscle via down‐regulation of nicotinamide N‐methyltransferase and autophagy is activated in the liver. These changes are supported by metabolite profiling which reveal elevated levels of many amino acids and spermidine in both liver and muscle and increased levels of NAD+ in muscle. The importance of MAF1 for metabolic economy reveals the potential for MAF1 modulators to protect against obesity and its harmful consequences.Support or Funding InformationThe work was supported by National Institutes of Health grants GM085177 (I.M.W.), AG043930 (J.A.), and T32 GM07491 (A.B.); the University of Lausanne, Swiss National Science Foundation grants 31003A_132958 (N.H.) and 31003A‐140780 (J.A.) and funds from the Albert Einstein College of Medicine.
Expression Analysis and Characterization of Tetratricopeptide Repeat Doman 39c (Ttc39c) in Skeletal Muscle
Authors: Waddell David , Menke Jacob 
Published: November 2023

Ttc39c has been identified as a novel gene in skeletal muscle that is differentially regulated under conditions of neurogenic atrophy in wild‐type mice compared to Muscle RING Finger 1 (MuRF1) knockout mice. MuRF1 is a ubiquitin E3 ligase that is known to be an important regulator of muscle wasting; however, evidence presented here suggests that MuRF1 may also function as a modulator of atrophy‐induced gene expression. Western blot analysis confirms that Ttc39c is expressed at the protein level in undifferentiated C2C12 myoblasts but is down‐regulated as cells differentiate to myotubes. Bioinformatic analysis of the Ttc39c gene locus reveals two alternative variants with distinct transcription initiation sites, which is an architecture that is conserved from rodents to humans. The transcriptional regulation of the shorter splice variant was examined by cloning the putative regulatory region and fusing it to a reporter gene. This reporter construct was then transfected into muscle cells along with an expression plasmid for MuRF1. MuRF1 overexpression repressed Ttc39c reporter activity, while overexpression of a MuRF1 RING domain mutant failed to repress the Ttc39c reporter. Furthermore, overexpression of myogenin, which is a myogenic regulatory factor (MRF) that regulates the expression of muscle‐specific genes by binding to E‐box elements, also repressed Ttc39c reporter gene activity. A conserved E‐box element in the Ttc39c proximal promoter was identified, mutated and analyzed for its role in the regulation of Ttc39c expression. The mutation of the conserved E‐box rendered the Ttc39c reporter gene inactive, demonstrating that the element is likely necessary for proper Ttc39c transcriptional regulation. The identification and characterization of novel genes that are activated during neurogenic atrophy helps improve our understanding of the molecular genetic events that lead to muscle wasting and could eventually lead to new therapeutic targets in the future.Support or Funding InformationUniversity of North Florida Transformational Learning Opportunity Grant
Transcriptional and translational regulation of CCAAT/Enhancer Binding Protein β expression by P53
Authors: Hu Biao , Wu Zhe , Bai David , Sheng Susanne , Phan Sem H 
Published: November 2023

The transcription factor CCAAT/enhancer‐binding protein β (C/EBPβ) is highly expressed in various tissues during development, including liver, adipose tissue, blood cells, lung and the endocrine pancreas. Two isoforms of C/EBPβ namely liver‐enriched activator protein (LAP) and liver‐enriched inhibitor protein (LIP) translated from the same mRNA have been described. The LAP and LIP isoforms share the same C‐terminal DNA binding domain except LAP has an extra N‐terminal activation domain. Probably due to its higher affinity for its DNA cognate sequences, the LIP can counteract the effects of LAP isoforms even at substoichiometric levels. In vitro and in vivo experiments with cultured cells and knockout mice demonstrated that C/EBPβ play a critical role in the regulation of myofibroblast differentiation and bleomycin induced pulmonary fibrosis. However, the regulatory mechanism of C/EBPβ gene expression is unclear. Analysis of the C/EBPβ promoter sequence identified a conserved P53 response element (P53RE) in the C/EBPβ gene promoter. Gel shift mobility and chromatin immunoprecipitation assays confirmed that P53 binds to the P53RE. Promoter reporter assays and real time PCR analysis of samples from fibroblasts transiently transfected with P53 or dominant negative P53 expression plasmids indicated that P53 was a repressor of C/EBPβ gene transcription. Western blot analysis with protein extracts from similarly transfected fibroblasts or P53 deficient fibroblasts showed that P53 differentially regulated translation of the C/EBPβ LAP and LIP isoforms through the regulation of eIF4E and eIF4E‐BP1. Further studies with constructs containing the LAP 5′ untranslated region or the LIP 5′ untranslated region showed that the 5′ untranslated region is important in differential control of C/EBPβ LAP and LIP translation. Thus P53 could regulate C/EBPβ gene expression at both transcriptional and translational levels.Support or Funding InformationThis work was supported by grants HL052285 and HL112880 from the National Institute of Health.
2‐Aminopurine is a Reporter for the Formation of the C·A+ Wobble Base Pair in U6 snRNA
Authors: Grossenbacher Max 
Published: November 2023

The spliceosome is a multimegadalton complex that is found in all eukaryotes and is involved in the excision of introns and ligation of exons to create mature RNA from pre‐mRNA. The U6 subunit of the spliceosome contains a highly conserved internal‐stem loop (ISL), which is essential to the activation and catalytic function of the spliceosome. The ISL has a 1X2 bulge that consists of a C67 ·A79+ wobble base pair (pKa 6.5) and an unpaired U80 nucleotide. The formation of C67· A79+ results in the base flipping of U80 out of the RNA helix, thus, stabilizing the formation of a continuous A‐form helix. At a pH above 6.5, U80 is stacked within the RNA helix, resulting in a bend in the helix that favors ion interactions. We examined the structural dynamics of U6 RNA using 2‐aminopurine (2‐AP), a fluorescent analog of adenine and guanine, that was substituted into U6 RNA constructs for A78. Thermal denaturation and fluorescent studies were used to measure the effects of pH and Mg2+ on the stability of U6 wild type RNA. Additionally, several modified constructs, including a control helix, were utilized to examine the role of nearby sequences on the formation of the C67 ·A79+ wobble base pair. Experiments were performed in 1M KCl and 10mM MgCl2 buffers in a pH range of 5.5 – 8.0. Thermal denaturation of U6 RNA constructs shows that the formation of C67 ·A79+ contributes ~1.0 kcal/mol of stability to U6 wild type RNA. Additionally, U6 wild type RNA shows a 2.2 kcal/mol increase in stability in 10mM MgCl2 buffer at pH 7.5, as compared to U6 wild type RNA in 1M KCl buffer.Support or Funding InformationNeena Grover & Colorado College Department of Biochemistry
The Interplay between S‐Palmitoylation and Gamma‐COP Binding of MAN1B1 Manages Alpha‐1‐Antitrypsin Quality Control
Authors: Young Evelin , Sifers Richard N. 
Published: November 2023

Genetic information is transformed into biological activity through the correct folding and proper deployment of encoded proteins. Numerous diseases result from complications caused by the failure of newly synthesized proteins to achieve these milestones. In Alpha‐1‐Antitrypsin Deficiency (AAT‐D), the toxic accumulation of aberrant AAT polymers in the hepatocyte secretory pathway is responsible for the development of childhood liver disease. Misfolded AAT monomers, which function as the direct precursor of toxic polymers, are subjected to proteasomal degradation in response to a poorly understood non‐enzymatic role of alpha‐1,2‐mannosidase, Class 1B, Member 1 (MAN1B1). In support of a role for MAN1B1 as a disease modifier, we have reported that a single nucleotide polymorphism in the corresponding gene that leads to the reduced expression of MAN1B1 is responsible for promoting the development of infantile end‐stage liver cirrhosis, the most severe form of AAT‐D. Importantly, MAN1B1, which can traffic between the Golgi complex and ER in response to the binding of gamma‐COP, promotes proteasomal degradation of the misfolded AAT monomer, designated NHK. However, it is presently unclear how the gamma‐COP‐mediated trafficking of MAN1B1 is regulated in order to govern the rate of ER‐associated degradation (ERAD) substrate recruitment. In the present study, we have uncovered that the amino‐terminal cytoplasmic tail of MAN1B1 is subjected to S‐palmitoylation. Mutation of the cysteine attachment sites enhanced the capacity of transfected MAN1B1 to degrade NHK, which coincided with an increased interaction with gamma‐COP. A novel posttranslational regulatory model is proposed in which the S‐palmitoylation of nearby cysteine residues functions to antagonize gamma‐COP binding, thereby hindering the retrograde trafficking and availability of MAN1B1, and reducing the proteasomal degradation of NHK by ERAD. Determining how to tip the balance of MAN1B1 to favor enhanced degradation of the misfolded AAT monomer is vital to the development of new therapeutic strategies for AAT‐D patients.Support or Funding InformationIRACDA K12‐GM084897 and Alpha‐1 Foundation
Development of Arginyl‐tRNA Synthetase from Pseudomonas aeruginosa as a Platform to Screen for Inhibitors of Protein Synthesis
Authors: Cantu Daniel , Salazar Humberto , Bullard James M 
Published: November 2023

IntroductionPseudomonas aeruginosa is a common cause of nosocomial infections and the leading cause of mortality in patents with cystic fibrosis. Aminoacyl‐tRNA synthetases (aaRSs) are a class of enzymes that catalyze the covalent attachment of amino acids to their cognate tRNAs during protein biosynthesis.ResultsP. aeruginosa arginyl‐tRNA synthetase (ArgRS) was overexpressed in Escherichia coli cells, and purified to homogeneity. ArgRS from P. aeruginosa is a discriminating synthetase with respect to the requirement for the presence of tRNAArg to produce a stable arginyl‐AMP intermediate. The kinetic parameters for interaction with tRNA were determined and the KM and Vmax were 4.0 μM and 11.7 μM min−1, respectively. The observed kcat was calculated to be 0.32 s−1 resulting in a kcat/KM value of 0.08 s−1μM−1. Scintillation proximity assay (SPA) technology was adapted to the aminoacylation assay and then used to screen for inhibitors of activity of P. aeruginosa ArgRS in a high throughput format. Using this assay, natural product (800 compounds) and synthetic compound (890 compounds) libraries were screened to detect compounds with the ability to inhibit function of the enzyme. Four compounds were identified which inhibit greater than 50% of enzymatic activity. Compounds BM06E07, BT04F10, BT10B04 and BT11F03 inhibit the activity of P. aeruginosa ArgRS with IC50 values of 29.2, 35.4, 31.6 and 8.1 μM, respectively. All four of these compounds exhibited promising MICs against Gram+ bacteria and moderate activity against Gram‐ bacteria causing respiratory infections.ConclusionArgRS identified in P. aeruginosa was cloned, expressed characterized and developed into a screening platform to identify compounds that have the potential for development as an antibacterial agent against pathogenic organisms.Support or Funding InformationResearch was funded by NIH grant 1SC3GM098173‐01A1. Partial student support was from a Departmental Grant from the Robert A. Welch Foundation (Grant No. BG‐0017).