bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shrinking the Mystery of Tsantsa Identification: Hair Analysis of Shrunken Heads from the Denver Museum of Nature and Science
Authors: Oya Mayu , Vinovskis Carissa , Royer Danielle 
Published: June 2021

INTRODUCTIONTribes in South America, such as the Jivaro, were historically known to perform shrinking of human heads as part of their war rituals. Although authentic shrunken heads (tsantsas) are of human origin, imitation tsantsas were later fabricated using animal or synthetic materials. Numerous tsantsas are held in museum collections worldwide, including five in the Anthropology Collection at the Denver Museum of Nature and Science (DMNS). A previous analysis of the tsantsas curated at the DMNS suggests that two specimens may be imitations.GOALSThe purpose of this study was to microscopically evaluate hairs from each of the five tsantsas in the Anthropology Collection at DMNS, and test the hypothesis that hairs from each specimen are human in origin.METHODSFive hairs from five different areas of the head (frontal, right and left temporal, vertex, occipital) were obtained for a total of 25 hairs per specimen. The hairs were mounted for microscopic analysis by researchers blinded to the origin of the samples. Using a brightfield microscope at 40x, images were collected using the Amscope image capture software and analyzed using ImageJ. The following qualitative characteristics were scored and compared to human norms: hair color, medulla features, cuticle thickness, pigment granule distribution, and the presence of scales. Measurements of hair shaft width and medulla width were also recorded for each hair and compared to human reference values for global populations.RESULTSThe qualitative analysis revealed that all of the hairs exhibited typical human characteristics. For each of the specimens, mean hair shaft and medulla width values were mostly within the normal range for human hair. However, a few exceptions were observed: 68% of sampled hairs from one specimen exhibited a medulla wider than expected for human hair, where the medulla is typically less than one‐third of the shaft width, and in another specimen, 72% of sampled hairs had shaft widths below the normal human range of 60–120um.CONCLUSIONWhen considering results from both the qualitative and quantitative analyses, the hairs from each of the DMNS tsantsas are likely to be human in origin. Previous analyses of the facial characteristics of the DMNS specimens suggested that two specimens may be imitations rather than authentic tsantsas. However, the hairs sampled from the two potential imitations appear to be human. It is possible that the genuine human hairs were manually imbedded into the scalp of the fabricated tsantsas; closer inspection of the internal scalp may provide insight. DNA analysis is needed to confirm the human origin of the tsantsas.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Sex Differences in the Effects of Prenatal Exposure to Low Doses of Endocrine Disruptors on Stress‐Related Behavior
Authors: Kaimal Amrita , Cherry Ariana D. , Martin Nicholas M. , Buechter Hannah E. , Hoover‐Smith Jessica M. , Holmes Philip V. , MohanKumar Sheba M. , Mohankumar P.S. 
Published: June 2021

Prenatal exposure to endocrine disrupting chemicals (EDCs) has been shown to produce a predisposition to behavioral disorders in later life. Bisphenol A (BPA) and di(2‐ethylhexyl) phthalate (DEHP) are two widely prevalent EDCs in the environment and exposure to these chemicals is unavoidable. We examined if prenatal exposure to these chemicals would produce behavioral changes in offspring. Female rats were orally administered BPA (B; 5 μg/kg body weight), DEHP (D; 7.5 mg/kg body weight), a combination of BPA and DEHP (B+D), or saline (control; 10 μL/kg body weight) during days 6 through 21 of pregnancy. Adult offspring underwent a battery of behavioral tests consisting of the open field task (OFT), elevated plus maze (EPM), and shock probe defensive burying (SPDB). In the OFT, control and B+D‐treated females spent a significantly lower percentage of time in the center zone than control males. These sex differences were not observed in B‐ or D‐treated animals, however, both male and female D‐offspring spent significantly less time in the center compared to control males. In the EPM, B animals displayed sex differences that were not present in control animals, with B females spending significantly more time in the open arms compared to both control and B males. D and B+D animals were not significantly different from controls in time spent in the open arms. No differences were seen in total exploration of the OFT or EPM. Control female animals reared and explored the probe significantly more than control males during SPDB. Sex differences were not present in B‐ or B+D‐treated offspring and were altered in D‐treated offspring. B‐treated female offspring buried less than control female offspring, but did not differ in immobility time or frequency of rearing or probe exploration in the SPDB, indicating a less robust response to threat. B treated male offspring were no different than control male offspring in the SPDB. D‐treated female offspring reared and explored the probe fewer times than female control‐treated offspring. Behavior was similar to control male offspring for each behavior, suggesting a masculinization of behavioral response to threat. D‐treated male offspring buried significantly less and spent significantly more time immobile than control males, suggesting a phenotypic shift to a passive‐coping style in response to threat. Finally, male and female B+D offspring showed a similar behavioral phenotype during SPDB. In conclusion, these results demonstrate that prenatal exposure to EDCs differentially alters behavior in male and female rats.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Analysis of Dendritic Spine Density in Hippocampus Following CA/CPR
Authors: Oya Mayu , Yonchek Joan , Quillinan Nidia 
Published: June 2021

INTRODUCTIONCardiac arrest (CA) occurs when the electrical system of the heart malfunctions. Patients do not receive enough blood to the brain and experience global cerebral ischemia, causing neuronal damage and affecting memory. The hippocampus is the main area of the brain dealing with learning and memory, and the dendrites and the spines of the CA1 neuron have been shown to undergo plasticity during learning and memory. Previous work has demonstrated that global cerebral ischemia causes persistent deficits in CA1 synaptic plasticity, but it is not known whether these deficits are associated with morphological changes. Acute dendritic plasticity (occurring within two to three days) after cardiac arrest/cardiopulmonary resuscitation (CA/CPR) have been shown previously. However, little is known regarding dendritic spine morphology at chronic time periods after CA/CPR.GOALThis present study investigated the plasticity of the CA1 neurons and their dendrites and spines in mice after CA/CPR.METHODSAdult male mice were given CA by intravenous injection of potassium chloride, and resuscitation was initiated eight minutes after arrest with chest compressions and ventilation. Mice were allowed to survive for one, seven, or 30 days after CA/CPR after which brains were collected. Whole brains were stained with Golgi‐cox staining technique, and sagittal sections were prepared for microscopy. High magnification images were taken on a bright field microscope using QCapture software and analyzed using ImageJ. The dendrites and their spines were observed in the CA1 region, and spine density, soma length, soma width, and soma area were calculated. Spines were also assigned a morphological classification (one to four) that ranges from immature to mature spines.RESULTSOur data shows that there is a significant reduction in spine densities at each of the time points after CA, compared to the sham. Furthermore, spine classification shows that CA caused a shift towards more immature spine morphology at 24 hours and 7 days after CA/CPR but shifted towards more mature spine morphology at 30 days after CA/CPR.CONCLUSIONThese data demonstrate that there is morphological plasticity and changes in dendritic spine anatomy at chronic time periods after CA/CPR. These changes likely correlate with synaptic plasticity impairments in the hippocampus.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The uracil‐DNA glycosylase homolog UdgX from M. smegmatis as a potential platform for in vitro protein evolution
Authors: Thomas Sydney Alexandra , Noren Chris 
Published: June 2021

A uracil‐DNA glycosylase (UDG) homolog from Mycobacterium smegmatis, UdgX, has been reported to lack uracil excision activity but instead binds uracil‐containing DNA tightly even under denaturing conditions, implying a covalent protein‐DNA adduct (Sang et al., “A unique uracil‐DNA binding protein of the uracil DNA glycosylase superfamily” NAR 43, 8452–63, 2015). To determine whether UdgX could be used as a fusion partner to tether a protein library to its encoding DNA as a platform for in vitro protein evolution, we expressed, purified, and characterized UdgX for its uracil‐binding activity. As expected, UdgX exhibits specific complex formation with uracil‐containing single stranded and double stranded DNA substrates by electrophoretic mobility shift assay (EMSA), but only in the absence of SDS. This implies that the UdgX‐DNA interaction is non‐covalent, contradicting the earlier report. Further work will be necessary to determine whether the noncovalent UdgX‐DNA interaction is sufficiently strong to stably tether a protein library to its encoding DNA.Support or Funding InformationNew England Biolabs Inc.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Comparison of Transcriptional Signature of Three Staphylococcal Superantigenic Toxins in Human Epidermal Melanocytes
Authors: Srinivasan Seshamalini , Chakraborty Nabarun , Miller Stacy‐Ann , Gautam Aarti , Yang Ruoting , Alkhalil Abdulnaser , Moffatt Lauren T. , jett Marti , Shupp Jeffrey W. , Hammamieh Rasha 
Published: June 2021

Staphylococcus aureus, a gram‐positive bacterium, causes food poisoning and toxic shock syndrome through the production of pyrogenic toxins known as Staphylococcal enterotoxins serotypes A‐J (SEA, SEB, etc.) and toxic shock syndrome toxin‐1 (TSST‐1). A subset of these toxins have been classified as potential biothreat agents and could effectively incapacitate the soldiers on the front line. The skin model was considered appropriate for this study as the skin is the first defense barrier for the host. The purpose of this research was to identify toxin‐exclusive network‐focused trajectories sequentially perturbed across time that could potentially characterize superantigenic toxicity and early pathogenesis. Normal Human Epidermal Melanocytes were grown and treated with 25 μg/mL of one of the three toxins, SEA, SEB, and TSST‐1. Cells were collected along with viability counts after being incubated for six different time periods ranging from 0.5h to 48h. Total RNA was purified using TRIzol reagent and oligonucleotide microarrays were performed using Agilent slides containing approximately 50,000 probes. Transcriptomic expression data indicated longitudinal trajectories unique to each of the three toxins. Transcriptomic responses to both SEA and TSST‐1 treatments had similar clustering patterns where early (0.5h, 2h), middle (6h, 12h) and late (24h, 48h) time points grouped together. Interestingly, genes responding to SEB treatment followed a different clustering profile where early (0.5h, 2h) and middle (6h, 12h, 24h) time points clustered together, and the latest time point (48h) was separate. Another interesting observation is that there were no shifts in the PCA landscape between the two late time points (24h, 48h) in response to SEA and TSST‐1 treatments, but this trend was not observed for the SEB treatment, which indicated a major transcriptomic perturbation between the 24h and 48h treatments. Therefore, we concluded that at the given doses, the progression of cellular responses to SEA and TSST‐1 treatment had completed by 24h while the SEB exposure continued to affect cellular responses until 48h.We have identified distinct patterns of transcriptomic regulation for each of the SEA, SEB and TSST‐1 toxins. Many of the differentially regulated genes have important functions related to cell transformation, differentiation, apoptosis and inflammation. Work is ongoing to identify differentially regulated networks with diagnostic and therapeutic implications.Disclaimer: Research was conducted in compliance with all Federal requirements. Views expressed are those of the authors and do not constitute endorsement by the U.S. Army.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Structural and Functional Effects of Altering the Nonpolar Core of Hemolysin A
Authors: Stuttgen Gage Michael , Weaver Todd Michael , Grilley Daniel Patrick 
Published: June 2021

The protein structure and function paradigm, a foundational tenet of biomolecular science, underlies many infectious diseases. Hemolysin A (HpmA), a hemolytic protein produced by Proteus mirabilis, was used as a model to investigate the protein structure‐function paradigm. HpmA is a member of the two‐partner secretion (TPS) pathway, which is used by gram‐negative bacteria to export predominantly virulent proteins outside of the cell. Through this mechanism, the A‐component (HpmA) is translocated, folded, and activated by its cognate B‐component in the absence of high‐energy bond and electrochemical gradient dependency. All TpsA components are relatively large and can be further divided into two domains, the two‐partner secretion domain and the functional domain. Universally, all known TPS domains harbor a right‐handed, parallel β‐helix architecture and are essential for cognate TpsB‐dependent recognition and secretion. Conversely, functional domains provide TpsA diversification including, cytolysis, host cell adhesion, contact‐growth inhibition, and iron sequestration. A truncated version of hemolysin A (HpmA265) was implemented to define the contributions of the TPS domain toward TpsA structure and function. Recently, our group has further dissected HpmA265 into three sequentially folded structural units termed the polar core, non‐polar core, and carboxy‐terminal subdomains. This research project aims to expand upon our recent results and structurally map the role of the nonpolar core during TPS domain dependent secretion, folding and function. Specifically, residues within the non‐polar core subdomain have been selectively targeted and modified. The structural and functional effects of these site‐selective modifications have been evaluated via chemical denaturation, protease sensitivity and hemolytic assays. Each site‐selective alteration selectively shifts the unfolding transitions attributed to the non‐polar core and carboxy‐terminal subdomain, while leaving the polar core transition unaffected. Furthermore, non‐polar core subdomain destabilization differentially alters secretion levels, while leaving hemolytic activity unaffected. More broadly, these results further define β‐helix TPS domain contribution during gram‐negative bacterial infections like whooping cough, meningitis, and urinary tract infections.Support or Funding InformationFunding for this research was provided by: University Wisconsin – La Crosse Faculty Research Grant Program (TMW) and University Wisconsin – La Crosse Undergraduate Research and Creativity Grant Program (GMS).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The Importance of Salt‐Bridge Formation of Lysine 52 and 54 from Apolipophorin III for Protein Structure and Function
Authors: Tran Angela , Shah Kriti , Weers Paul M.M. 
Published: June 2021

Apolipophorin III (apoLp‐III) is an 18 kDa exchangeable apolipoprotein found in insects. The protein is used as a model to better understand lipid transport processes and innate immunity due to the availability of three‐dimensional structures of the protein, allowing a structure‐guided approach. ApoLp‐III from Locusta migratoria contains eight lysine residues, which interact with negatively charged phospholipids found in bacterial membranes. They also help to maintain the structure of the protein by ionic interactions. Denaturation of the protein with guanidine‐HCl showed that when lysine residues at position 52 and 54 were changed into glutamine, protein stability was significantly reduced. To identify which of the two lysine residues are involved in salt bridge formation with neighboring glutamate or aspartate residues, site‐directed mutagenesis was employed to design single lysine to glutamine (KQ) variants. The K52Q and K54Q single mutants were generated using the Quick‐change site‐directed mutagenesis kit. E. coli cells were transformed with the mutant plasmids, and protein expression was induced by IPTG. SDS‐PAGE analysis of the bacterial cultures showed the presence of apoLp‐III in the media, indicating that the proteins escaped the bacteria. Upon purification by reversed‐phase HPLC the structure of the mutant proteins will be assessed using circular dichroism to determine helical content and protein stability, while phosphatidylglycerol bilayer vesicles will be used for functional studies. Identification of the salt‐bridge in apoLp‐III will help to better understand the role of ionic interactions in the structure and function of apolipoproteins.Support or Funding InformationThis research was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Numbers GM089564, 8UL1GM118979‐02, 8TL4GM118980‐02, and 8RL5GM118978‐02.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Identifying Residue‐Residue Contacts via Deep Mutational Scanning
Authors: Hinds Emily C. , Romero Philip A. 
Published: June 2021

Structural knowledge is critical for understanding a protein's biological function and interactions, aiding drug design and other advances in medicine and biotechnology. However, there are many proteins for which structural data are either of poor quality or completely absent, and the inefficiency of experimental structure determination necessitates computational approaches to address this gap. The accuracy of de novo folding simulations in full‐length structure prediction can be improved by incorporating information about individual pairs of contacting residues. But if the full structure is not known, often the true structural contacts are also unknown. These contacts can be inferred from an evolutionary alignment of sequences by identifying residues that are co‐mutated, but this approach is greatly limited by the amount of data available. With the rise of ultrahigh‐throughput functional screening and sequencing techniques, large alignments of functionally active sequences can be generated to provide comprehensive mutational data. Here, we demonstrate that contact information can be obtained from a set of active β‐glucosidases identified via deep mutational scanning. To identify residues for which mutations are coupled and therefore may be in contact, we calculated mutual information for all residue pairs in the set of active sequences. Within this set, relatively high mutual information correlates with residues closer in structure. Preliminary de novo modeling simulations in Rosetta show that only a subset of true contacts are necessary for fold‐level predictive accuracy. We expect additional work to confirm that the predicted contacts of β‐glucosidase support accurate de novo structure prediction. Thus, we have formed a foundation to investigate the applications of ultrahigh‐throughput functional screening in protein structure prediction. With a wealth of sequences, quality contact information can be more readily acquired, fueling accurate structure prediction for continued medical and biotechnological development.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Determining Chaperone Requirements for the Propagation of Heterologous Poly‐Glutamine Aggregates in Saccharomyces cerevisiae
Authors: Killian Andrea N. , Cole Sierra J. , Hines Justin K. 
Published: June 2021

Amyloid‐based yeast prions are heritable aggregates of misfolded protein that can be passed on to daughter cells following fragmentation by chaperone proteins including Hsp70, Hsp104, and the Hsp40 Sis1. Yeast prions usually exhibit an amyloid structure, forming cross‐beta sheets of protein sections known as the prion‐forming domain, or PrD. In vivo, long tracts of glutamine have been shown to form amyloid structures. Previously Alexandrov et al. created a set of polyQ sequences with a single heterologous amino acid interspersed every fifth residue (QQQXQ), fused to the MC regions of yeast Sup35 (responsible for the prion [PSI+]) and expressed in a sup35‐ΔN strain of Saccharomyces cerevisiae. These polyQX sequences replace the PrD of Sup35, and form amyloid aggregates in vivo that propagate in an Hsp104‐dependent manner. Here we report our efforts to test the J‐protein chaperone requirements of these aggregates, first by repressing levels of Sis1 to determine if any polyQX aggregates are maintained without Sis1. Preliminary results suggest several QX constructs are dependent upon Sis1 for propagation, demonstrating that these aggregates propagate in an Hsp40/Hsp70‐dependent manner. Subsequent replacement of wild‐type Sis1 expression with several well‐studied Sis1 variants will allow the determination of the importance of specific regions of Sis1 for the propagation of these aggregates. We anticipate that this line of investigation will provide significant insight into the ways in which amino acid content of a PrD affects the interaction of the resulting prion with chaperone proteins.Support or Funding InformationThis work was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R15GM110606. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.