Mortality Patterns of Asian Elephants in a Region of Human–Elephant Conflict

Many wildlife species suffer from human–wildlife conflict, especially crop-raiding. Long-term analyses of mortality patterns are needed to assess the efficacy of management strategies that address this issue. We report mortality patterns from necropsies of 498 Asian elephants from 2009–2018 in an area of northwestern Sri Lanka. Deaths were lowest in July and highest in October, a period of peak crop availability. Most (about 70%) deaths were human-related, and males were killed in these incidents more frequently than females. As gunshot deaths decreased, other forms of human-related deaths increased. Additionally, causes of death differed between districts, with more intentional human-related mortality observed in the district with the highest percent of protected land. These results highlight the importance of understanding the long-term spatial and temporal variation in wildlife mortality to effectively address human–wildlife conflict. © 2021 The Wildlife Society.     

Attenuation of Inflammation by DJ-1 May Be a Drug Target for Cerebral Ischemia–Reperfusion Injury

Neurochemical Research - The pathophysiological process of cerebral apoplexy is complex, and there are currently no specific drugs for this condition. The study of effective drug targets has become...     

The Relative Contribution of Proximal 5′ Flanking Sequence and Microsatellite Variation on Brain Vasopressin 1a Receptor (Avpr1a) Gene Expression and Behavior

Certain genes exhibit notable diversity in their expression patterns both within and between species. One such gene is the vasopressin receptor 1a gene (Avpr1a), which exhibits striking differences in neural expression patterns that are responsible for mediating differences in vasopressin-mediated social behaviors. The genomic mechanisms that contribute to these remarkable differences in expression are not well understood. Previous work has suggested that both the proximal 5′ flanking region and a polymorphic microsatellite element within that region of the vole Avpr1a gene are associated with variation in V1a receptor (V1aR) distribution and behavior, but neither has been causally linked. Using homologous recombination in mice, we reveal the modest contribution of proximal 5′ flanking sequences to species differences in V1aR distribution, and confirm that variation in V1aR distribution impacts stress-coping in the forced swim test. We also demonstrate that the vole Avpr1a microsatellite structure contributes to Avpr1a expression in the amygdala, thalamus, and hippocampus, mirroring a subset of the inter- and intra-species differences observed in central V1aR patterns in voles. This is the first direct evidence that polymorphic microsatellite elements near behaviorally relevant genes can contribute to diversity in brain gene expression profiles, providing a mechanism for generating behavioral diversity both at the individual and species level. However, our results suggest that many features of species-specific expression patterns are mediated by elements outside of the immediate 5′ flanking region of the gene.     

Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence

Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10⁻¹⁵). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant F_ST (p = 0.00003) and positive Tajima''s D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human–Neandertal divergence and is evolving under balancing selection, especially among European populations.     

Isolation of a Tomato Protease that May Be Involved in Proteolysis of 1-Aminocyclopropane-l-Carboxylate Synthase

1-aminocyclopropane- 1-carboxylate （ACC） synthase is a principal enzyme that catalyses the committed step in phytohormone ethylene biosynthesis. Previous evidence indicates that the hypervariable C-terminus of ACC synthase is most likely to be processed proteolytically in vivo. However, the protease responsible has not been identified thus far. In the present study, we detected proteolytic activity against ACC synthase （LeACS2） in tomato （Lycopersicon esculentum Mill.） fruit extract based on a newly established in vitro assay system. Purification of the protease through DEAE, gel filtration and MonoQ chromatography resulted in considerable enrichment of a 64-kDa protein species. Subsequent biochemical analysis of the purified tomato protease revealed that the optimal conditions for its proteolytic activity were at pH 8.0 and at 37 ~C. In addition, the protease activity was blocked completely by the metalloprotease inhibitor 1,10-phenanthroline. The present study represents the first report on the isolation of an ACC synthase- processing protease from plant tissues.     

Quantification of IGF-1 Receptor May Be Useful in Diagnosing Polycythemia Vera–Suggestion to Be Added to Be One of the Minor Criterion

Endogenous erythroid colony (EEC) formation is one of the minor criteria for diagnosing polycythemia vera (PV) according to 2008 WHO diagnostic criteria. But EEC requires bone marrow aspiration and sophisticated laboratory procedures; therefore, practically it is rarely used to diagnose PV. Insulin-like growth factor 1 receptor (IGF-1R) was found to be constitutively phosphorylated and was responsible for the EEC formation in PV; therefore, we measured IGF-1R levels in the peripheral blood of 26 PV patients and compared them with those of 33 patients with secondary polycythemia and 29 normal controls. Among the PV patients, 16 were treated with only phlebotomy, 9 received hydroxyurea, and 1 was treated with ruxolinitinib. We found that PV patients treated with only phlebotomy had significantly higher IGF-1R levels than did those PV patients treated with hydroxyurea or ruxolinitinib. None of the secondary PV patients or normal controls had elevated IGR-1R levels, while 14 of 16 (87%) PV patients had significantly elevated IGF-1R levels. The new 2016 WHO has eliminated EEC as a minor criterion for diagnosing PV, but there are still some cases that cannot be definitively diagnosed by the current criteria. Therefore, we suggest that quantifying the IGF-1R level in peripheral blood by flow cytometry to replace EEC as the minor criterion for diagnosing PV.     

Searching for Spatial Patterns in a Pollinator–Plant–Herbivore Mathematical Model

This paper deals with the spatio-temporal dynamics of a pollinator–plant–herbivore mathematical model. The full model consists of three nonlinear reaction–diffusion–advection equations defined on a rectangular region. In view of analyzing the full model, we firstly consider the temporal dynamics of three homogeneous cases. The first one is a model for a mutualistic interaction (pollinator–plant), later on a sort of predator–prey (plant–herbivore) interaction model is studied. In both cases, the interaction term is described by a Holling response of type II. Finally, by considering that the plant population is the unique feeding source for the herbivores, a mathematical model for the three interacting populations is considered. By incorporating a constant diffusion term into the equations for the pollinators and herbivores, we numerically study the spatiotemporal dynamics of the first two mentioned models. For the full model, a constant diffusion and advection terms are included in the equation for the pollinators. For the resulting model, we sketch the proof of the existence, positiveness, and boundedness of solution for an initial and boundary values problem. In order to see the separated effect of the diffusion and advection terms on the final population distributions, a set of numerical simulations are included. We used homogeneous Dirichlet and Neumann boundary conditions.     

Spatiotemporal Variation in Bonobo (Pan paniscus) Habitat Use in a Forest–Savanna Mosaic

International Journal of Primatology - Understanding the ecological and behavioral variation of primates is central to improving conservation strategies. Studies of chimpanzees (Pan troglodytes)...     

Regional Variations in Esophageal Cancer Rates by Census Region in the United States, 1999–2008

Background

Assessment of cancer incidence trends within the U.S. have mostly relied upon Surveillance, Epidemiology, and End Results (SEER) data, with implicit inference that such is representative of the general population. However, many cancer policy decisions are based at a more granular level. To help inform such, analyses of regional cancer incidence data are needed. Leveraging the unique resource of National Program of Cancer Registries (NPCR)-SEER, we assessed whether regional rates and trends of esophageal cancer significantly deviated from national estimates.

Methods

From NPCR-SEER, we extracted cancer case counts and populations for whites aged 45–84 years by calendar year, histology, sex, and census region for the period 1999–2008. We calculated age-standardized incidence rates (ASRs), annual percent changes (APCs), and male-to-female incidence rate ratios (IRRs).

Results

This analysis included 65,823 esophageal adenocarcinomas and 27,094 esophageal squamous cell carcinomas diagnosed during 778 million person-years. We observed significant geographic variability in incidence rates and trends, especially for esophageal adenocarcinomas in males: ASRs were highest in the Northeast (17.7 per 100,000) and Midwest (18.1). Both were significantly higher than the national estimate (16.0). In addition, the Northeast APC was 62% higher than the national estimate (3.19% vs. 1.97%). Lastly, IRRs remained fairly constant across calendar time, despite changes in incidence rates.

Conclusion

Significant regional variations in esophageal cancer incidence trends exist in the U.S. Stable IRRs may indicate the predominant factors affecting incidence rates are similar in men and women.     

Augmentation of Autoantibodies by Helicobacter pylori in Parkinson’s Disease Patients May Be Linked to Greater Severity

Parkinson''s disease (PD) is the second most common chronic and progressive neurodegenerative disorder. Its etiology remains elusive and at present only symptomatic treatments exists. Helicobacter pylori chronically colonizes the gastric mucosa of more than half of the global human population. Interestingly, H. pylori positivity has been found to be associated with greater of PD motor severity. In order to investigate the underlying cause of this association, the Sengenics Immunome protein array, which enables simultaneous screening for autoantibodies against 1636 human proteins, was used to screen the serum of 30 H. pylori-seropositive PD patients (case) and 30 age- and gender-matched H. pylori-seronegative PD patients (control) in this study. In total, 13 significant autoantibodies were identified and ranked, with 8 up-regulated and 5 down-regulated in the case group. Among autoantibodies found to be elevated in H. pylori-seropositive PD were included antibodies that recognize Nuclear factor I subtype A (NFIA), Platelet-derived growth factor B (PDGFB) and Eukaryotic translation initiation factor 4A3 (eIFA3). The presence of elevated autoantibodies against proteins essential for normal neurological functions suggest that immunomodulatory properties of H. pylori may explain the association between H. pylori positivity and greater PD motor severity.     

Substrate Compositional Variation with Tissue/Region and Gba1 Mutations in Mouse Models–Implications for Gaucher Disease

Gaucher disease results from GBA1 mutations that lead to defective acid β-glucosidase (GCase) mediated cleavage of glucosylceramide (GC) and glucosylsphingosine as well as heterogeneous manifestations in the viscera and CNS. The mutation, tissue, and age-dependent accumulations of different GC species were characterized in mice with Gba1 missense mutations alone or in combination with isolated saposin C deficiency (C*). Gba1 heteroallelism for D409V and null alleles (9V/null) led to GC excesses primarily in the visceral tissues with preferential accumulations of lung GC24∶0, but not in liver, spleen, or brain. Age-dependent increases of different GC species were observed. The combined saposin C deficiency (C*) with V394L homozygosity (4L;C*) showed major GC18∶0 degradation defects in the brain, whereas the analogous mice with D409H homozygosity and C* (9H;C*) led to all GC species accumulating in visceral tissues. Glucosylsphingosine was poorly degraded in brain by V394L and D409H GCases and in visceral tissues by D409V GCase. The neonatal lethal N370S/N370S genotype had insignificant substrate accumulations in any tissue. These results demonstrate age, organ, and mutation-specific quantitative differences in GC species and glucosylsphingosine accumulations that can have influence in the tissue/regional expression of Gaucher disease phenotypes.     

Spontaneous and Engineered Deletions in the 3′ Noncoding Region of Tick-Borne Encephalitis Virus: Construction of Highly Attenuated Mutants of a Flavivirus

The flavivirus genome is a positive-strand RNA molecule containing a single long open reading frame flanked by noncoding regions (NCR) that mediate crucial processes of the viral life cycle. The 3′ NCR of tick-borne encephalitis (TBE) virus can be divided into a variable region that is highly heterogeneous in length among strains of TBE virus and in certain cases includes an internal poly(A) tract and a 3′-terminal conserved core element that is believed to fold as a whole into a well-defined secondary structure. We have now investigated the genetic stability of the TBE virus 3′ NCR and its influence on viral growth properties and virulence. We observed spontaneous deletions in the variable region during growth of TBE virus in cell culture and in mice. These deletions varied in size and location but always included the internal poly(A) element of the TBE virus 3′ NCR and never extended into the conserved 3′-terminal core element. Subsequently, we constructed specific deletion mutants by using infectious cDNA clones with the entire variable region and increasing segments of the core element removed. A virus mutant lacking the entire variable region was indistinguishable from wild-type virus with respect to cell culture growth properties and virulence in the mouse model. In contrast, even small extensions of the deletion into the core element led to significant biological effects. Deletions extending to nucleotides 10826, 10847, and 10870 caused distinct attenuation in mice without measurable reduction of cell culture growth properties, which, however, were significantly restricted when the deletion was extended to nucleotide 10919. An even larger deletion (to nucleotide 10994) abolished viral viability. In spite of their high degree of attenuation, these mutants efficiently induced protective immune responses even at low inoculation doses. Thus, 3′-NCR deletions represent a useful technique for achieving stable attenuation of flaviviruses that can be included in the rational design of novel flavivirus live vaccines.The genus Flavivirus (family Flaviviridae) consists of small, enveloped, mainly mosquito- or tick-transmitted viruses with an unsegmented positive-stranded RNA genome (34). Some of these viruses are human pathogens of global medical importance, most notably yellow fever virus, the dengue (DEN) viruses, Japanese encephalitis virus, and tick-borne encephalitis (TBE) virus (22). In spite of the availability of vaccines against several of these viruses, flavivirus infections continue to be a major health problem in many countries of the world. Elucidation of the molecular basis of the pathogenicity of these viruses and identification of specific determinants of virulence are therefore a major focus of flavivirus research.The approximately 11-kb flavivirus genome (for a review, see reference 3) encodes three structural proteins (the capsid protein C, the small membrane protein M, which is formed by proteolytic cleavage from its precursor protein prM, and the large envelope protein E) and seven nonstructural proteins (the glycoprotein NS1, the protease component NS2A, NS2B, the protease/helicase NS3, NS4A, NS4B, and the RNA polymerase NS5). All of the viral proteins are encoded within a single long open reading frame which is flanked by noncoding regions (NCR) believed to carry regulatory elements involved in replication, translation, and packaging of the genome. Molecular analyses of natural low-virulence strains and strains attenuated in vitro by passaging procedures or, more recently, by specific mutagenesis techniques, have shown that genetic determinants that govern the virulence of flaviviruses are located within the coding regions of both structural and nonstructural proteins as well as within the flanking NCRs (2, 21, 26; for reviews, see references 20 and 22). In this study, we focus on the effects of deletions in the 3′ noncoding region (3′ NCR) of TBE virus.TBE virus causes widespread human disease in many European and Asian countries, and its molecular biology has been studied in some detail (29; for a review, see reference 9). The length of the 3′ NCR of TBE virus was previously found to be remarkably heterogeneous even among closely related strains, ranging from approximately 450 to almost 800 nucleotides (31). A more detailed analysis indicated that the 3′ NCR can be divided into a 3′-terminal core element of approximately 340 nucleotides in length and a variable region located between the core element and the open reading frame. The core element is present in all strains investigated so far, and its nucleotide sequence is highly conserved among strains. The entire core element is predicted to fold into a well-defined secondary structure independent of the sequence of the adjacent variable genomic element (27). The variable region is characterized by low sequence conservation, extensive size variability between strains, repetitive sequence elements, and an internal poly(A) tract in certain TBE virus strains (15, 31). Evidence for 3′-NCR size heterogeneity and specific RNA-folding patterns for the 3′-terminal approximately 400 nucleotides have also been observed with several other flaviviruses (5, 24, 25, 33). A similar organization of the 3′ NCRs also appears to be shared by members of the other two genera of the family Flaviviridae, pestiviruses and hepaciviruses (13, 23, 30, 35).Although the functional importance of the flavivirus 3′ NCR is generally acknowledged, the assumed involvement of particular sequence elements in replication, modulation of translation, or packaging is largely hypothetical. Evidence for functionality is so far based mostly on the identification of highly conserved RNA sequence elements or folding patterns by computer techniques. A few studies have provided direct evidence for the binding of protein factors to the stem-loop structure closest to the 3′ terminus (1, 4). Moreover, Men et al. (21) demonstrated that certain deletions introduced into the 3′ NCR of DEN-4 virus resulted in viable mutants with significantly restricted growth properties. By this approach, these researchers were able to identify particular sequences that are required for viability and others that can be deleted without apparent impact on the biology of DEN-4 virus. Studying replicons of Kunjin virus, Khromykh and Westaway (14) found that parts of the 3′ NCR could be deleted or even replaced by a foreign protein expression cassette without loss of replication competence. The 3′-NCR sequences of these flaviviruses, however, exhibit very little homology to the sequences of the tick-borne flaviviruses, which even lack the sequence boxes CS1 and CS2 that are conserved among all mosquito-borne flaviviruses (7, 16).The establishment of an efficient and stable infectious cDNA clone system for TBE virus European subtype prototypic strain Neudoerfl (17) has enabled us to test the functional importance of 3′-NCR sequence elements of this virus by a directed mutagenesis approach. As reported in this communication, spontaneous deletions in the variable region of strain Neudoerfl occur frequently during viral growth in cell culture or in infected animals. This prompted us to construct 3′-NCR deletion mutants of variable lengths to study the influence of these deletions on the biological properties of TBE virus. Our results demonstrate a correlation between the presence of certain RNA sequences or secondary structures and growth properties, viability, and attenuation of the resulting virus mutants. We present several 3′-NCR deletion mutants that are 4 orders of magnitude less virulent than wild-type TBE virus.With regard to vaccine development, the most desirable mutations are ones that are genetically stable and cause significant attenuation but maintain adequate replication properties in cell culture and strong immunogenicity in animals even at low inoculation doses. The evaluation of the TBE virus mutants presented in this article indicates that certain deletions in the 3′ NCR can indeed meet these criteria.     

Deletions in Xq26.3–q27.3 including FMR1 result in a severe phenotype in a male and variable phenotypes in females depending upon the X inactivation pattern

High resolution cytogenetics, microsatellite marker analyses, and fluorescence in situ hybridization were used to define Xq deletions encompassing the fragile X gene, FMR1, detected in individuals from two unrelated families. In Family 1, a 19-year-old male had facial features consistent with fragile X syndrome; however, his profound mental and growth retardation, small testes, and lover limb skeletal defects and contractures demonstrated a more severe phenotype, suggestive of a contiguous gene syndrome. A cytogenetic deletion including Xq26.3–q27.3 was observed in the proband, his phenotypically normal mother, and his learning-disabled non-dysmorphic sister. Methylation analyses at the FMR1 and androgen receptor loci indicated that the deleted X was inactive in > 95% of his mother’s white blood cells and 80–85% of the sister’s leukocytes. The proximal breakpoint for the deletion was approximately 10 Mb centromeric to FMR1, and the distal breakpoint mapped 1 Mb distal to FMR1. This deletion, encompassing ∼13 Mb of DNA, is the largest deletion including FMR1 reported to date. In the second family, a slightly smaller deletion was detected. A female with moderate to severe mental retardation, seizures, and hypothyroidism, had a de novo cytogenetic deletion extending from Xq26.3 to q27.3, which removed ∼12 Mb of DNA around the FMR1 gene. Cytogenetic and molecular data revealed that ∼50% of her white blood cells contained an active deleted X. These findings indicate that males with deletions including Xq26.3–q27.3 may exhibit a more severe phenotype than typical fragile X males, and females with similar deletions may have an abnormal phenotype if the deleted X remains active in a significant proportion of the cells. Thus, important genes for intellectual and neurological development, in addition to FMR1, may reside in Xq26.3–q27.3. One candidate gene in this region, SOX3, is thought to be involved in neuronal development and its loss may partly explain the more severe phenotypes of our patients. Received: 19 December 1996 / Accepted: 13 March 1997     

Patterns in self-rated health according to age and sex in a Japanese national survey, 1989–2004

Background: Perceived good health or good self-rated health is considered to be a predictor of longer survival and maintenance of good quality of life, which is a public health goal.Objective: This study assessed trends in the percentage of self-rated poor health among Japanese residents, based on data from the National Comprehensive Survey of the Living Conditions of People on Health and Welfare.Methods: Results of the survey (which is conducted in Japan every 3 years to determine the living conditions of people receiving health and welfare services) were analyzed using multistage and stratified cluster sampling of households. Self-rated health was measured by response to the question, “Recently, would you say that in general your health has been good, fairly good, fair, fairly poor, or poor?” The trend in fairly poor or poor health status during the period from 1989 through 2004 was stratified by sex and age group.Results: The rates of response to the survey were 90.9% (246,892/271,588) in 1995 and 79.8% (220,836/276,682) in 2004. Target subjects were aged ≥20 years in each year of the study. The prevalence of self-reported fairly poor or poor health was lowest in 1995 and then increased every year until 2001, when it appeared to reach a plateau. The prevalence of having fairly poor or poor health among women aged 35 to 44, 45 to 54, 55 to 64, and 65 to 74 years were as follows in 1995: 9.2%, 11.7%, 15.3%, and 19.8%, respectively. In 2004, the rates were 13.3%, 17.2%, 22.1%, and 31.7%, respectively. By comparison, the prevalence of self-reported fairly poor or poor health was 8.1%, 9.3%, 13.7%, and 17.9% among men aged 35 to 44, 45 to 54, 55 to 64, and 65 to 74 years, respectively, in 1995. In 2004, these rates were 12.8%, 14.8%, 19.0%, and 27.9%, respectively.Conclusions: In this survey, conducted every 3 years between 1989 and 2004 in Japanese households, older subjects had a greater prevalence of self-reported fairly poor or poor health than did younger subjects. The proportion of respondents who described their health as poor or fairly poor was highest in 1995. Women generally had a greater prevalence of self-reported poor or fairly poor health.     

Nascent β Structure in the Elongated Hydrophobic Region of a Gerstmann–Sträussler–Scheinker PrP Allele

Prion diseases are neurodegenerative disorders caused by the misfolding of the cellular prion protein (PrP^C). Gerstmann–Sträussler–Scheinker syndrome is an inherited prion disease with one early-onset allele (HRdup) containing an eight-amino-acid insertion; this LGGLGGYV insert is positioned after valine 129 (human PrP^C sequence) in a hydrophobic tract in the natively disordered region. Here we have characterized the structure and explored the molecular motions and dynamics of HRdup PrP and a control allele. High-resolution NMR data suggest that the core of HRdup has a canonical PrP^C structure, yet a nascent β-structure is observed in the flexible elongated hydrophobic region of HRdup. In addition, using mouse PrP^C sequence, we observed that a methionine/valine polymorphism at codon 128 (equivalent of methionine/valine 129 in human sequence) and oligomerization caused by high protein concentration affects conformational exchange dynamics at residue G130. We hypothesize that with the β-structure at the N-terminus, the hydrophobic region of HRdup can adopt a fully extended configuration and fold back to form an extended β-sheet with the existing β-sheet. We propose that these structures are early chemical events in disease pathogenesis.