Physical activity and temperature changes of Asian elephants (Elephas maximus) participating in eco-tourism activities and elephant polo.

Captive and domestic animals are often required to engage in physical activity initiated or organised by humans, which may impact their body temperature, with consequences for their health and welfare. This is a particular concern for animals such as elephants that face thermoregulatory challenges because of their body size and physiology. Using infrared thermography, we measured changes in skin temperature associated with two types of physical activity in ten female Asian elephants (Elephas maximus) at an eco-tourism lodge in Nepal. Six elephants took part in an activity relatively unfamiliar to the elephants-a polo tournament-and four participated in more familiar ecotourism activities. We recorded skin temperatures for four body regions affected by the activities, as well as an average skin temperature. Temperature change was used as the response variable in the analysis and calculated as the difference in elephant temperature before and after activity. We found no significant differences in temperature change between the elephants in the polo-playing group and those from the non-polo playing group. However, for both groups, when comparing the average skin body temperature and several different body regions, we found significant differences in skin temperature change before and after activity. The ear pinna was the most impacted region and was significantly different to all other body regions. This result highlights the importance of this region in thermoregulation for elephants during physical activity. However, as we found no differences between the average body temperatures of the polo and non-polo playing groups, we suggest that thermoregulatory mechanisms can counteract the effects of both physical activities the elephants engaged in.

Human interventions in a behavioural experiment for Asian Elephants (Elephas maximus).

Experiments are widely used to investigate the behaviour and cognition of animals. While the automation of experiments to avoid potential experimenter bias is sometimes possible, not all experiments can be conducted without human presence. This is particularly true for large animals in captivity, which are often managed by professional handlers. For the safety of the animals and experimenters, a handler must be present during behavioural studies with certain species. It is not always clear to what extent cues provided by handlers affect the animals, and therefore the experimental results. In this study, we investigate handler interventions during the training process for a behavioural experiment with Asian elephants (Elephas maximus) in Nepal. We show that elephant handlers (mahouts) intervened to guide elephants in performing the learning task using vocal and behavioural cues, despite experimenters requesting minimal intervention. We found that although the frequency of mahout interventions did not decrease as the training progressed, the nature of their interventions changed. We also found more non-verbal than verbal cues across the training. Our results suggest that guidance from handlers may be common in behavioural studies, and continued consideration should be put into experimental design to reduce or account for cues that animals may receive from humans. This study also emphasises the need to take into account the presence of humans in interpreting the results of animal behavioural experiments, which not only presents challenges to behavioural research, but also represents opportunities for further study.

Discussion of wildlife trade before and during the COVID-19 pandemic in professional opinion pieces and scientific articles.

Wildlife trade is a multi-billion-dollar sector that impacts a wide range of species, and thus is of significant research and conservation interest. Wildlife trade has also become a prominent topic in the public-facing media, where coverage has intensified following the outbreak of the global COVID-19 pandemic due to the potential connection between wildlife trade and the origin of the SARS Cov2 virus. Given the importance of the media in shaping public understanding and discourse of complex topics such as wildlife trade, this could impact the implementation of and public support for policy decisions. In this study, we followed a standardised protocol to extract wildlife trade-related discussion from 285 professional opinion pieces (NGO reports or articles in conservation-themed forums) and 107 scientific articles published in two time periods: "pre-COVID" (June 1-December 31, 2019) and "during-COVID" (January 1-May 31, 2020). We compared opinion pieces and scientific articles across the two time periods and to each other to investigate potential differences in the presentation of wildlife trade and associated speakers. We found a shift in the way that wildlife trade was discussed in professional opinion pieces between the periods, in that the discussion became less specific in terms of defining the legality and purpose of trade, and the animal groups involved in the "during-COVID" period. The generalised framing of wildlife trade in our dataset also coincided with an increased discussion of highly generalised management strategies, such as blanket bans on wildlife trade. We also found that publications included more quotes from researchers in the "during-COVID" period. In both professional opinion pieces and scientific articles, we found that quotations or research were often from speakers whose affiliation region was different to the geographic range of the trade they were speaking about. This highlights the importance of incorporating local knowledge and considering the diversity of speakers and interviewees in both research and the public-facing media about the wildlife trade.

Noninvasive Detection of Microsatellite Instability and High Tumor Mutation Burden in Cancer Patients Treated with PD-1 Blockade.

PURPOSE: Microsatellite instability (MSI) and high tumor mutation burden (TMB-High) are promising pan-tumor biomarkers used to select patients for treatment with immune checkpoint blockade; however, real-time sequencing of unresectable or metastatic solid tumors is often challenging. We report a noninvasive approach for detection of MSI and TMB-High in the circulation of patients. EXPERIMENTAL DESIGN: We developed an approach that utilized a hybrid-capture-based 98-kb pan-cancer gene panel, including targeted microsatellite regions. A multifactorial error correction method and a novel peak-finding algorithm were established to identify rare MSI frameshift alleles in cell-free DNA (cfDNA). RESULTS: Through analysis of cfDNA derived from a combination of healthy donors and patients with metastatic cancer, the error correction and peak-finding approaches produced a specificity of >99% (n = 163) and sensitivities of 78% (n = 23) and 67% (n = 15), respectively, for MSI and TMB-High. For patients treated with PD-1 blockade, we demonstrated that MSI and TMB-High in pretreatment plasma predicted progression-free survival (hazard ratios: 0.21 and 0.23, P = 0.001 and 0.003, respectively). In addition, we analyzed cfDNA from longitudinally collected plasma samples obtained during therapy to identify patients who achieved durable response to PD-1 blockade. CONCLUSIONS: These analyses demonstrate the feasibility of noninvasive pan-cancer screening and monitoring of patients who exhibit MSI or TMB-High and have a high likelihood of responding to immune checkpoint blockade.See related commentary by Wang and Ajani, p. 6887.

Direct detection of early-stage cancers using circulating tumor DNA.

Early detection and intervention are likely to be the most effective means for reducing morbidity and mortality of human cancer. However, development of methods for noninvasive detection of early-stage tumors has remained a challenge. We have developed an approach called targeted error correction sequencing (TEC-Seq) that allows ultrasensitive direct evaluation of sequence changes in circulating cell-free DNA using massively parallel sequencing. We have used this approach to examine 58 cancer-related genes encompassing 81 kb. Analysis of plasma from 44 healthy individuals identified genomic changes related to clonal hematopoiesis in 16% of asymptomatic individuals but no alterations in driver genes related to solid cancers. Evaluation of 200 patients with colorectal, breast, lung, or ovarian cancer detected somatic mutations in the plasma of 71, 59, 59, and 68%, respectively, of patients with stage I or II disease. Analyses of mutations in the circulation revealed high concordance with alterations in the tumors of these patients. In patients with resectable colorectal cancers, higher amounts of preoperative circulating tumor DNA were associated with disease recurrence and decreased overall survival. These analyses provide a broadly applicable approach for noninvasive detection of early-stage tumors that may be useful for screening and management of patients with cancer.

Classification and automatic transcription of primate calls.

This paper reports on an automated and openly available tool for automatic acoustic analysis and transcription of primate calls, which takes raw field recordings and outputs call labels time-aligned with the audio. The system's output predicts a majority of the start times of calls accurately within 200 milliseconds. The tools do not require any manual acoustic analysis or selection of spectral features by the researcher.

Semi-Quantitative Analysis of Inherent Visible Particles for Biopharmaceutical Products.

Visible particles must be monitored as part of the control strategy for pharmaceutical products. Extraneous (foreign) particles are not acceptable in parenteral drug products. In biopharmaceuticals, formation of protein particles is recognized as an inherent quality attribute. All protein therapeutics contain particles that vary greatly in visibility and size from invisible (sub-micron) to visible (millimeter) and, as part of the control strategy, biopharmaceutical companies are required to monitor and minimize the presence of visible and sub-visible particles in their products. There is an industry-wide unmet need for particle standards for visual inspection of protein therapeutics. A new, semi-quantitative method using particle standards for assessing the levels of small, inherent visible particles is presented. This method can be used during product development to identify a formulation that minimizes particle formation and also during release and stability testing to monitor and control inherent proteinaceous visible particles. LAY ABSTRACT: Visible particles must be monitored as part of the control strategy for parenteral biopharmaceutical drug products. In these products, formation of protein particles is a natural occurrence. All protein drugs contain particles that vary greatly in visibility and size from invisible (sub-micron) to visible (millimeter), and pharmaceutical companies are required to monitor and minimize the presence of visible and sub-visible particles in their products. There is an industry-wide unmet need for particle standards for visual inspection of protein drugs. A new, semi-quantitative method using particle standards for assessing the levels of small, naturally occurring visible particles is presented. This method can be used during drug development to identify a formulation that minimizes particle formation and also during testing of final clinical or commercial drug product to monitor and control naturally occurring proteinaceous visible particles.

Clinical implications of genomic alterations in the tumour and circulation of pancreatic cancer patients.

Pancreatic adenocarcinoma has the worst mortality of any solid cancer. In this study, to evaluate the clinical implications of genomic alterations in this tumour type, we perform whole-exome analyses of 24 tumours, targeted genomic analyses of 77 tumours, and use non-invasive approaches to examine tumour-specific mutations in the circulation of these patients. These analyses reveal somatic mutations in chromatin-regulating genes MLL, MLL2, MLL3 and ARID1A in 20% of patients that are associated with improved survival. We observe alterations in genes with potential therapeutic utility in over a third of cases. Liquid biopsy analyses demonstrate that 43% of patients with localized disease have detectable circulating tumour DNA (ctDNA) at diagnosis. Detection of ctDNA after resection predicts clinical relapse and poor outcome, with recurrence by ctDNA detected 6.5 months earlier than with CT imaging. These observations provide genetic predictors of outcome in pancreatic cancer and have implications for new avenues of therapeutic intervention.

Personalized genomic analyses for cancer mutation discovery and interpretation.

Massively parallel sequencing approaches are beginning to be used clinically to characterize individual patient tumors and to select therapies based on the identified mutations. A major question in these analyses is the extent to which these methods identify clinically actionable alterations and whether the examination of the tumor tissue alone is sufficient or whether matched normal DNA should also be analyzed to accurately identify tumor-specific (somatic) alterations. To address these issues, we comprehensively evaluated 815 tumor-normal paired samples from patients of 15 tumor types. We identified genomic alterations using next-generation sequencing of whole exomes or 111 targeted genes that were validated with sensitivities >95% and >99%, respectively, and specificities >99.99%. These analyses revealed an average of 140 and 4.3 somatic mutations per exome and targeted analysis, respectively. More than 75% of cases had somatic alterations in genes associated with known therapies or current clinical trials. Analyses of matched normal DNA identified germline alterations in cancer-predisposing genes in 3% of patients with apparently sporadic cancers. In contrast, a tumor-only sequencing approach could not definitively identify germline changes in cancer-predisposing genes and led to additional false-positive findings comprising 31% and 65% of alterations identified in targeted and exome analyses, respectively, including in potentially actionable genes. These data suggest that matched tumor-normal sequencing analyses are essential for precise identification and interpretation of somatic and germline alterations and have important implications for the diagnostic and therapeutic management of cancer patients.

Increased Expression of Phosphorylated FADD in Anaplastic Large Cell and Other T-Cell Lymphomas.

FAS-associated protein with death domain (FADD) is a major adaptor protein involved in extrinsic apoptosis, embryogenesis, and lymphocyte homeostasis. Although abnormalities of the FADD/death receptor apoptotic pathways have been established in tumorigenesis, fewer studies have analyzed the expression and role of phosphorylated FADD (pFADD). Our identification of FADD as a lymphoma-associated autoantigen in T-cell lymphoma patients raises the possibility that pFADD, with its correlation with cell cycle, may possess role(s) in human T-cell lymphoma development. This immunohistochemical study investigated pFADD protein expression in a range of normal tissues and lymphomas, particularly T-cell lymphomas that require improved therapies. Whereas pFADD was expressed only in scattered normal T cells, it was detected at high levels in T-cell lymphomas (eg, 84% anaplastic large cell lymphoma and 65% peripheral T cell lymphomas, not otherwise specified). The increased expression of pFADD supports further study of its clinical relevance and role in lymphomagenesis, highlighting phosphorylation of FADD as a potential therapeutic target.

RNASET2--an autoantigen in anaplastic large cell lymphoma identified by protein array analysis.

Characterising tumour-associated antigens (TAAs) not only represents an important approach to the identification of new diagnostic/prognostic markers, but can also provide information on disease processes and additional potential therapeutic targets. Preliminary screening of a protein macroarray, containing more than 12,000 different proteins, with sera from anaplastic lymphoma kinase (ALK)-negative and ALK-positive anaplastic large cell lymphoma (ALCL) patients identified ribonuclease and tumour suppressor protein Ribonuclease T2 (RNASET2), phosphatase lipid phosphate phosphatase-related protein type 3 (LPPR3) and apoptotic adaptor molecule Fas-associating protein (FADD) as ALK-negative ALCL-associated TAAs. Further validation of these observations was confirmed using the ALCL sera in reverse ELISAs. The circulating anti-RNASET2 autoantibodies present in ALCL patients' sera also recognised eukaryotically expressed RNASET2 protein. RNASET2 expression was then investigated in normal tissues and in lymphomas to explore its clinical potential. RNASET2 protein and mRNA levels showed highest expression in the spleen, leucocytes and pancreas. RNASET2 protein expression was not restricted to ALK-negative ALCL (81%), being expressed in ALK-positive ALCL (65%) as well as in a number of other lymphomas. The immunological recognition of RNASET2, its expression in ALCL and other lymphomas together with its known tumourigenic properties suggest that further studies on this autoantigen are warranted.

MiRNA-335 suppresses neuroblastoma cell invasiveness by direct targeting of multiple genes from the non-canonical TGF-ß signalling pathway.

Transforming growth factor-ß (TGF-ß) signaling regulates many diverse cellular activities through both canonical (SMAD-dependent) and non-canonical branches, which includes the mitogen-activated protein kinase (MAPK), Rho-like guanosine triphosphatase and phosphatidylinositol-3-kinase/AKT pathways. Here, we demonstrate that miR-335 directly targets and downregulates genes in the TGF-ß non-canonical pathways, including the Rho-associated coiled-coil containing protein (ROCK1) and MAPK1, resulting in reduced phosphorylation of downstream pathway members. Specifically, inhibition of ROCK1 and MAPK1 reduces phosphorylation levels of the motor protein myosin light chain (MLC) leading to a significant inhibition of the invasive and migratory potential of neuroblastoma cells. Additionally, miR-335 targets the leucine-rich alpha-2-glycoprotein 1 (LRG1) messenger RNA, which similarly results in a significant reduction in the phosphorylation status of MLC and a decrease in neuroblastoma cell migration and invasion. Thus, we link LRG1 to the migratory machinery of the cell, altering its activity presumably by exerting its effect within the non-canonical TGF-ß pathway. Moreover, we demonstrate that the MYCN transcription factor, whose coding sequence is highly amplified in a particularly clinically aggressive neuroblastoma tumor subtype, directly binds to a region immediately upstream of the miR-335 transcriptional start site, resulting in transcriptional repression. We conclude that MYCN contributes to neuroblastoma cell migration and invasion, by directly downregulating miR-335, resulting in the upregulation of the TGF-ß signaling pathway members ROCK1, MAPK1 and putative member LRG1, which positively promote this process. Our results provide novel insight into the direct regulation of TGF-ß non-canonical signaling by miR-335, which in turn is downregulated by MYCN.

Protein tyrosine phosphatase receptor delta acts as a neuroblastoma tumor suppressor by destabilizing the aurora kinase A oncogene.

BACKGROUND: Protein tyrosine phosphatase receptor delta (PTPRD) is a member of a large family of protein tyrosine phosphatases which negatively regulate tyrosine phosphorylation. Neuroblastoma is a major childhood cancer arising from precursor cells of the sympathetic nervous system which is known to acquire deletions and alterations in the expression patterns of PTPRD, indicating a potential tumor suppressor function for this gene. The molecular mechanism, however, by which PTPRD renders a tumor suppressor effect in neuroblastoma is unknown. RESULTS: As a molecular mechanism, we demonstrate that PTPRD interacts with aurora kinase A (AURKA), an oncogenic protein that is over-expressed in multiple forms of cancer, including neuroblastoma. Ectopic up-regulation of PTPRD in neuroblastoma dephosphorylates tyrosine residues in AURKA resulting in a destabilization of this protein culminating in interfering with one of AURKA's primary functions in neuroblastoma, the stabilization of MYCN protein, the gene of which is amplified in approximately 25 to 30% of high risk neuroblastoma. CONCLUSIONS: PTPRD has a tumor suppressor function in neuroblastoma through AURKA dephosphorylation and destabilization and a downstream destabilization of MYCN protein, representing a novel mechanism for the function of PTPRD in neuroblastoma.

Developmental changes in the engagement of episodic retrieval processes and their relationship with working memory during the period of middle childhood.

We examined the development of children's engagement of the episodic retrieval processes of recollection and familiarity and their relationship with working memory (WM). Ninety-six children (24 in four groups aged 8, 9, 10, and 11 years) and 24 adults performed an episodic memory (EM) task involving old/new, remember/know (R/K), and source memory judgements and numerous WM tasks that assessed verbal and spatial components of WM and delayed short-term memory (STM). Developmental changes were observed in EM with younger children (8-, 9-, 10-year-olds) making fewer remember responses than 11-year-olds and adults while 11-year-olds did not differ from adults. Only children aged 10 years plus showed a relationship between EM and WM. EM was related to verbal executive WM in 10- and 11-year-old children suggesting that children at this stage use verbal strategies to aid EM. In contrast, EM was related to spatial executive WM in adults. The engagement of episodic retrieval processes appears to be selectively related to executive components of verbal and spatial WM, the pattern of which differs in children and adults.

Numerical Estimation in Deaf and Hearing Adults.

Deaf students often lag behind hearing peers in numerical and mathematical abilities. Studies of hearing children with mathematical difficulties highlight the importance of estimation skills as the foundation for formal mathematical abilities, but research with adults is limited. Deaf and hearing college students were assessed on the Number-to-Position task as a measure of estimation, and completed standardised assessments of arithmetical and mathematical reasoning. Deaf students performed significantly more poorly on all measures, including making less accurate number-line estimates. For deaf students, there was also a strong relationship showing that those more accurate in making number-line estimates achieved higher scores on the math achievement tests. No such relationship was apparent for hearing students. Further insights into the estimation abilities of deaf individuals should be made, including tasks that require symbolic and non-symbolic estimation and which address the quality of estimation strategies being used.

Co-localization of the oncogenic transcription factor MYCN and the DNA methyl binding protein MeCP2 at genomic sites in neuroblastoma.

BACKGROUND: MYCN is a transcription factor that is expressed during the development of the neural crest and its dysregulation plays a major role in the pathogenesis of pediatric cancers such as neuroblastoma, medulloblastoma and rhabdomyosarcoma. MeCP2 is a CpG methyl binding protein which has been associated with a number of cancers and developmental disorders, particularly Rett syndrome. METHODS AND FINDINGS: Using an integrative global genomics approach involving chromatin immunoprecipitation applied to microarrays, we have determined that MYCN and MeCP2 co-localize to gene promoter regions, as well as inter/intragenic sites, within the neuroblastoma genome (MYCN amplified Kelly cells) at high frequency (70.2% of MYCN sites were also positive for MeCP2). Intriguingly, the frequency of co-localization was significantly less at promoter regions exhibiting substantial hypermethylation (8.7%), as determined by methylated DNA immunoprecipitation (MeDIP) applied to the same microarrays. Co-immunoprecipitation of MYCN using an anti-MeCP2 antibody indicated that a MYCN/MeCP2 interaction occurs at protein level. mRNA expression profiling revealed that the median expression of genes with promoters bound by MYCN was significantly higher than for genes bound by MeCP2, and that genes bound by both proteins had intermediate expression. Pathway analysis was carried out for genes bound by MYCN, MeCP2 or MYCN/MeCP2, revealing higher order functions. CONCLUSIONS: Our results indicate that MYCN and MeCP2 protein interact and co-localize to similar genomic sites at very high frequency, and that the patterns of binding of these proteins can be associated with significant differences in transcriptional activity. Although it is not yet known if this interaction contributes to neuroblastoma disease pathogenesis, it is intriguing that the interaction occurs at the promoter regions of several genes important for the development of neuroblastoma, including ALK, AURKA and BDNF.

Dissection of the oncogenic MYCN transcriptional network reveals a large set of clinically relevant cell cycle genes as drivers of neuroblastoma tumorigenesis.

Amplification of the oncogenic transcription factor MYCN plays a major role in the pathogenesis of several pediatric cancers, including neuroblastoma, medulloblastoma, and rhabodomyosarcoma. For neuroblastoma, MYCN amplification is the most powerful genetic predictor of poor patient survival, yet the mechanism by which MYCN drives tumorigenesis is only partially understood. To gain an insight into the distribution of MYCN binding and to identify clinically relevant MYCN target genes, we performed an integrated analysis of MYCN ChIP-chip and mRNA expression using the MYCN repressible SHEP-21N neuroblastoma cell line. We hypothesized that genes exclusively MYCN bound in SHEP-21N cells over-expressing MYCN would be enriched for direct targets which contribute to the process of disease progression. Integrated analysis revealed that MYCN drives tumorigenesis predominantly as a positive regulator of target gene transcription. A high proportion of genes (24%) that are MYCN bound and up-regulated in the SHEP-21N model are significantly associated with poor overall patient survival (OS) in a set of 88 tumors. In contrast, the proportion of genes down-regulated when bound by MYCN in the SHEP-21N model and which are significantly associated with poor overall patient survival when under-expressed in primary tumors was significantly lower (5%). Gene ontology analysis determined a highly statistically significant enrichment for cell cycle related genes within the over-expressed MYCN target group which were also associated with poor OS. We conclude that the over-expression of MYCN leads to aberrant binding and over-expression of genes associated with cell cycle regulation which are significantly correlated with poor OS and MYCN amplification.

MicroRNA mediates DNA demethylation events triggered by retinoic acid during neuroblastoma cell differentiation.

Neuroblastoma is an often fatal pediatric cancer arising from precursor cells of the sympathetic nervous system. 13-Cis retinoic acid is included in the treatment regimen for patients with high-risk disease, and a similar derivative, all-trans-retinoic acid (ATRA), causes neuroblastoma cell lines to undergo differentiation. The molecular signaling pathways involved with ATRA-induced differentiation are complex, and the role that DNA methylation changes might play are unknown. The purpose of this study was to evaluate the genome-wide effects of ATRA on DNA methylation using methylated DNA immunoprecipitation applied to microarrays representing all known promoter and CpG islands. Four hundred and two gene promoters became demethylated, whereas 88 were hypermethylated post-ATRA. mRNA expression microarrays revealed that 82 of the demethylated genes were overexpressed by >2-fold, whereas 13 of the hypermethylated genes were underexpressed. Gene ontology analysis indicated that demethylated and re-expressed genes were enriched for signal transduction pathways, including NOS1, which is required for neural cell differentiation. As a potential mechanism for the DNA methylation changes, we show the downregulation of methyltransferases, DNMT1 and DNMT3B, along with the upregulation of endogenous microRNAs targeting them. Ectopic overexpression of miR-152, targeting DNMT1, also negatively affected cell invasiveness and anchorage-independent growth, contributing in part to the differentiated phenotype. We conclude that functionally important, miRNA-mediated DNA demethylation changes contribute to the process of ATRA-induced differentiation resulting in the activation of NOS1, a critical determinant of neural cell differentiation. Our findings illustrate the plasticity and dynamic nature of the epigenome during cancer cell differentiation.

Protein interactions with the platelet integrin alpha(IIb) regulatory motif.

Integrins are transmembrane proteins regulating cellular shape, mobility and the cell cycle. A highly conserved signature motif in the cytoplasmic tail of the integrin alpha-subunit, KXGFFKR, plays a critical role in regulating integrin function. To date, six proteins have been identified that target this motif of the platelet-specific integrin alpha(IIb)beta(3). We employ peptide-affinity chromatography followed-up with LC-MS/MS analysis as well as protein chips to identify new potential regulators of integrin function in platelets and put them into their biological context using information from protein:protein interaction (PPI) databases. Totally, 44 platelet proteins bind with high affinity to an immobilized LAMWKVGFFKR-peptide. Of these, seven have been reported in the PPI literature as interactors with integrin alpha-subunits. 68 recombinant human proteins expressed on the protein chip specifically bind with high affinity to biotin-tagged alpha-integrin cytoplasmic peptides. Two of these proteins are also identified in the peptide-affinity experiments, one is also found in the PPI databases and a further one is present in the data to all three approaches. Finally, novel short linear interaction motifs are common to a number of proteins identified.