Patterns and trends in two decades of research on Nepal’s mammalian fauna (2000–2019): examining the past for future implications

Nepal is a global biodiversity hotspot, supporting 213 mammal species with diverse habitats across various landscape types, from the lowland Terai to the high Himalayas. Studies of Nepal’s mammalian fauna are not evenly distributed and better understanding of past biases towards some species, research themes and locations can provide better strategic direction for future research investments. Therefore, we reviewed 575 scientific articles on mammals in Nepal, published between 2000 and 2019 and compiled these in March 2020, to examine trends, patterns and gaps, and pave future plans for mammalian research in Nepal. A positive increase in the number of publications (β?=?0.27?±?0.02SD, P?<?0.00) was observed, with a more than threefold increase between 2010 and 2019 compared to 2000–2009 (t?=?? 6.26, df?=?12.21, P?<?0.000). Analysis of these documents revealed that mammalian researches favored large flagship, threatened species of carnivores inside Nepal’s protected area system. Geographically, mammalian research was not uniform in Nepal, as most studies were concentrated in Bagmati Province and in the Terai and Chure region. Baseline surveys and ecological studies were more common types of research, while studies on the impact of climate change and wildlife trade and poaching, are scant, which deserves a future look. While these studies shape current mammalogy in Nepal, studies of small, uncharismatic species, and in areas outside protected areas and other provinces except Bagmati, Lumbini and Province One are severely lacking. The research identified habitat loss, degradation and human-wildlife conflict as the major threats to the survival of mammalian species in Nepal. Therefore, redesigning and strict implementation of policies based on habitat management and human-wildlife co-existence, including other threat mitigation measures, are warranted. To address knowledge gaps, the prioritization of future research and funding should be focused on relatively unexplored research themes and under-researched provinces. This approach will help to re-align the research focus with the current need, and assist to fully understand and effectively conserve the wealth of mammalian diversity that Nepal holds.

     

Assessing loss of coral cover on Australia’s Great Barrier Reef over two decades, with implications for longer-term trends

While coral reefs in many parts of the world are in decline as a direct consequence of human pressures, Australia’s Great Barrier Reef (GBR) is unusual in that direct human pressures are low and the entire system of ~2,900 reefs has been managed as a marine park since the 1980s. In spite of these advantages, standard annual surveys of a large number of reefs showed that from 1986 to 2004, average live coral cover across the GBR declined from 28 to 22%. This overall decline was mainly due to large losses in six (21%) of 29 subregions. Declines in live coral cover on reefs in two inshore subregions coincided with thermal bleaching in 1998, while declines in four mid-self subregions were due to outbreaks of predatory starfish. Otherwise, living coral cover increased in one subregion (3%) and 22 subregions (76%) showed no substantial change. Reefs in the great majority of subregions showed cycles of decline and recovery over the survey period, but with little synchrony among subregions. Two previous studies examined long-term changes in live coral cover on GBR reefs using meta-analyses including historical data from before the mid-1980s. Both found greater rates of loss of coral and recorded a marked decrease in living coral cover on the GBR in 1986, coinciding exactly with the start of large-scale monitoring. We argue that much of the apparent long-term decrease results from combining data from selective, sparse, small-scale studies before 1986 with data from both small-scale studies and large-scale monitoring surveys after that date. The GBR has clearly been changed by human activities and live coral cover has declined overall, but losses of coral in the past 40–50 years have probably been overestimated.     

Effects of oxysterols on the blood–brain barrier: Implications for Alzheimer’s disease

Altered brain cholesterol homeostasis plays a key role in neurodegenerative diseases such as Alzheimer’s disease (AD). For a long time, the blood–brain barrier (BBB) was basically considered as a barrier isolating the brain from circulating cholesterol, however, several lines of evidence now suggest that the BBB strictly regulates the exchanges of sterol between the brain and the peripheral circulation. Oxysterols, synthesized by neurons or by peripheral cells, cross the BBB easily and modulate the expression of several enzymes, receptors and transporters which are involved not only in cholesterol metabolism but also in other brain functions. This review article deals with the way oxysterols impact BBB cells. These perspectives open new routes for designing certain therapeutical approaches that target the BBB so that the onset and/or progression of brain diseases such as AD may be modulated.     

Nitrogen budgets of the Polish agriculture 1960–2000: implications for riverine nitrogen loads to the Baltic Sea from transitional countries

The Oder and the Vistula rivers are responsible for about 25% of the total riverine nitrogen input to the Baltic Sea and of this 60% have been estimated to originate from diffuse sources. In this study we have tested the hypothesis that changes in agricultural practices in Poland have changed the riverine nitrogen export from the rivers Oder and Vistula to the Baltic Sea. We calculated agricultural long-term nitrogen budgets (1960–2000) for the catchments of the Oder and the Vistula rivers. Poland went through severe economical changes in the early 1990s, which led to a drastic decrease in fertilizer consumption. The role of the calculated nitrogen surplus as an eutrophication capacitor and the potential to reduce this important capacitor to improve the environmental state of the Baltic Sea is discussed. N surplus for the entire country showed a maximum in 1980 (58 kg ha⁻¹ sown area⁻¹) and it dropped to 39 kg ha⁻¹ sown area⁻¹ in 2000. The surplus was, however, up to two times lower than that in other transitional countries, and much lower than in Western Europe with intensive agriculture. An observed decrease in nitrogen concentrations in both Polish rivers is not ascribed to drop in fertilizer use, but it results from nutrient removal in municipal wastewater treatment plants with tertiary treatment facilities. Comparison of trends in nitrogen concentrations in different transition countries indicates that factors other than reduced fertilizer application influenced the inertia of the water quality response. Hence, the potential to reduce diffuse nitrogen emissions from agriculture by reducing fertilization is constricted in areas with low-nitrogen surplus. In transitional countries like Poland the largest potential for nutrient reductions seem to be in improving the connectivity to waste water treatment plants with tertiary treatment.     

A step on the path in the discovery of new latent fingerprint development reagents: substituted Ruhemann’s purples and implications for the law

Energies corresponding to optimum geometries of ninhydrin, some of its analogs, the corresponding Ruhemann’s Purple analogs and some of the intermediates of the reaction between ninhydrin analogs and amino acids are calculated at Hartree–Fock/6-31G** level of theory. Such a study is significant from a forensic science point of view because of the strong interest in the forensic chemistry and law enforcement communities in developing alternatives to the current generation of ninhydrin-like chemicals for the detection and development of latent fingerprints. In examining our new predictions for the net energetics of the reactions in the formation of substituted Ruhemann’s Purples, we find that a fluorine-containing analog is the most thermodynamically feasible reaction. In light of this finding, we suggest further experimental studies to determine the kinetic feasibility of synthesizing the fluorine-containing analog, as well as other similar molecules and to determine their spectroscopic properties.     

Hilgendorf’s (1863) dissertation on the steinheim planorbids (Gastropoda; Miocene): The development of a phylogenetic research program for paleontology

Hilgendorf’s (1866) publication on the phylogenyof Planorbis multiformis from Steinheim, Swabian Mountains, is one of the most important contributions of paleontology to early Darwinism. At the same time it helped to lay the foundation for paleontological phylogenetics. Hilgendorf’s unpublished dissertation of 1863, the newly rediscovered collection to his dissertation and the document-file ofHilgendorf’s graduation from Tübingen University help to trace back the origin of Hilgendorf’s ideas.Hilgendorf’s collection contains the oldest phylogenetic tree, which is known so far.     

Heavy metals toxicity: effect of cadmium ions on amyloid beta protein 1–42. Possible implications for Alzheimer’s disease

Cadmium (Cd) is an environmental contaminant, highly toxic to humans. This biologically non-essential element accumulates in the body, especially in the kidney, liver, lung and brain and can induce several toxic effects, depending on the concentration and the exposure time. Cd has been linked to Alzheimer’s disease (AD) as a probable risk factor, as it shows higher concentrations in brain tissues of AD patients than in healthy people, its implication in the formation of neurofibrillary tangles and in the aggregation process of amyloid beta peptides (AβPs). AβPs seem to have toxic properties, particularly in their aggregated state; insoluble AβP forms, such as small and large aggregates, protofibrils and fibrils, appear to be implicated in the pathogenesis of AD. In our study, we have evaluated the effect of Cd, at different concentrations, both on the AβP1–42 ion channel incorporated in a planar lipid membrane made up of phosphatidylcholine containing 30 % cholesterol and on the secondary structure of AβP1–42 in aqueous environment. Cadmium is able to interact with the AβP1–42 peptide by acting on the channel incorporated into the membrane as well as on the peptide in solution, both decreasing AβP1–42 channel frequency and in solution forming large and amorphous aggregates prone to precipitate. These experimental observations suggesting a toxic role for Cd strengthen the hypothesis that Cd may interact directly with AβPs and may be a risk factor in AD.     

Clinical practice vs. state-of-the-art research and future visions: Report on the 4D treatment planning workshop for particle therapy – Edition 2018 and 2019

The 4D Treatment Planning Workshop for Particle Therapy, a workshop dedicated to the treatment of moving targets with scanned particle beams, started in 2009 and since then has been organized annually. The mission of the workshop is to create an informal ground for clinical medical physicists, medical physics researchers and medical doctors interested in the development of the 4D technology, protocols and their translation into clinical practice. The 10th and 11th editions of the workshop took place in Sapporo, Japan in 2018 and Krakow, Poland in 2019, respectively.This review report from the Sapporo and Krakow workshops is structured in two parts, according to the workshop programs. The first part comprises clinicians and physicists review of the status of 4D clinical implementations. Corresponding talks were given by speakers from five centers around the world: Maastro Clinic (The Netherlands), University Medical Center Groningen (The Netherlands), MD Anderson Cancer Center (United States), University of Pennsylvania (United States) and The Proton Beam Therapy Center of Hokkaido University Hospital (Japan). The second part is dedicated to novelties in 4D research, i.e. motion modelling, artificial intelligence and new technologies which are currently being investigated in the radiotherapy field.     

Neuroprotective effects of human mesenchymal stem cells on neural cultures exposed to 6-hydroxydopamine: implications for reparative therapy in Parkinson’s disease

Stem cell (SC) transplantation represents a promising tool to treat neurodegenerative disorders, such as Parkinson's disease (PD), but positive therapeutic outcomes require elucidation of the biological mechanisms involved. Therefore, we investigated human Mesenchymal SCs (hMSCs) ability to protect murine differentiated Neural SCs (mdNSCs) against the cytotoxic effects of 6-hydroxydopamine (6-OHDA) in a co-culture model mimicking the in vivo neurovascular niche. The internalization of 6-OHDA mainly relies on its uptake by the dopamine active transporter (DAT), but its toxicity could also involve other pathways. We demonstrated that mdNSCs consistently expressed DAT along the differentiative process. Exposure to 6-OHDA did not affect hMSCs, but induced DAT-independent apoptosis in mdNSCs with generation of reactive oxygen species and caspases 3/7 activation. The potential neuroprotective action of hMSCs on mdNSCs exposed to 6-OHDA was tested in different co-culture conditions, in which hMSCs were added to mdNSCs prior to, simultaneously, or after 6-OHDA treatment. In the presence of the neurotoxin, the majority of mdNSCs acquired an apoptotic phenotype, while co-cultures with hMSCs significantly increased their survival (up to 70%) in all conditions. Multiplex human angiogenic array analysis on the conditioned media demonstrated that cytokine release by hMSCs was finely modulated. Moreover, sole growth factor addition yielded a similar neuroprotective effect on mdNSCs. In conclusion, our findings demonstrate that hMSCs protect mdNSCs against 6-OHDA neurotoxicity, and rescue cells from ongoing neurodegeneration likely through the release of multiple cytokines. Our findings provide novel insights for the development of therapeutic strategies designed to counteract the neurodegenerative processes of PD.     

Two decades of tropical cyclone impacts on North Carolina’s estuarine carbon,nutrient and phytoplankton dynamics: implications for biogeochemical cycling and water quality in a stormier world

Coastal North Carolina (USA) has experienced 35 tropical cyclones over the past 2 decades; the frequency of these events is expected to continue in the foreseeable future. Individual storms had unique and, at times, significant hydrologic, nutrient-, and carbon (C)-loading impacts on biogeochemical cycling and phytoplankton responses in a large estuarine complex, the Pamlico Sound (PS) and Neuse River Estuary (NRE). Major storms caused up to a doubling of annual nitrogen and tripling of phosphorus loading compared to non-storm years; magnitudes of loading depended on storm tracks, forward speed, and precipitation in NRE-PS watersheds. With regard to C cycling, NRE-PS was a sink for atmospheric CO₂ during dry, storm-free years and a significant source of CO₂ in years with at least one storm, although responses were storm-specific. Hurricane Irene (2011) mobilized large amounts of previously-accumulated terrigenous C in the watershed, mainly as dissolved organic carbon, and extreme winds rapidly released CO₂ to the atmosphere. Historic flooding after Hurricanes Joaquin (2015) and Matthew (2016) provided large inputs of C from the watershed, modifying the annual C balance of NRE-PS and leading to sustained CO₂ efflux for months. Storm type affected biogeochemical responses as C-enriched floodwaters enhanced air–water CO₂ exchange during ‘wet’ storms, while CO₂ fluxes during ‘windy’ storms were largely supported by previously-accumulated C. Nutrient loading and flushing jointly influenced spatio-temporal patterns of phytoplankton biomass and composition. These findings suggest the importance of incorporating freshwater discharge and C dynamics in nutrient management strategies for coastal ecosystems likely to experience a stormier future.     

The new sequencer on the block: comparison of Life Technology’s Proton sequencer to an Illumina HiSeq for whole-exome sequencing

We assessed the performance of the new Life Technologies Proton sequencer by comparing whole-exome sequence data in a Centre d’Etude du Polymorphisme Humain trio (family 1463) to the Illumina HiSeq instrument. To simulate a typical user’s results, we utilized the standard capture, alignment and variant calling methods specific to each platform. We restricted data analysis to include the capture region common to both methods. The Proton produced high quality data at a comparable average depth and read length, and the Ion Reporter variant caller identified 96 % of single nucleotide polymorphisms (SNPs) detected by the HiSeq and GATK pipeline. However, only 40 % of small insertion and deletion variants (indels) were identified by both methods. Usage of the trio structure and segregation of platform-specific alleles supported this result. Further comparison of the trio data with Complete Genomics sequence data and Illumina SNP microarray genotypes documented high concordance and accurate SNP genotyping of both Proton and Illumina platforms. However, our study underscored the problem of accurate detection of indels for both the Proton and HiSeq platforms.     

From molecules to the biosphere: Nikolai V. Timoféeff-Ressovsky’s (1900–1981) research program within a totalitarian landscape

Nikolai Vladimirovich Timoféeff-Ressovsky was one of the key figures in the Synthetic Theory of Evolution. Living and researching under what was arguably the two most powerful and cruel totalitarian regimes in human history, the Third Reich and the Soviet Union, Timoféeff-Ressovsky succeeded in developing an ambitious research program aiming to explain evolution on all major levels, from the molecular-genetic, the populational, and the biogeocenotic to the level of the entire Biosphere. Yet his scientific biography remains largely unwritten and his role under totalitarianism, especially in Nazi Germany, remains highly controversial. Here we approach the problem of his hypothetical cooperation with Nazi authorities examining both the crucial episodes of his biography and summarizing the development of his research program. We conclude that the key decisions he made reflected the specificity of his research program that was focused on the fundamental questions of evolutionary biology.     

LigPath: a module for predictive calculation of a ligand’s pathway into a receptor-application to the gpH<Subscript>1</Subscript> - receptor

Until now, the access of ligands into the binding pocket of a G-protein coupled receptor has scarcely been studied using molecular-modeling techniques because of the lack of sufficient algorithms. Neither with Monte-Carlo- nor with Molecular Dynamics Simulations can the penetration of a ligand into the binding pocket of a receptor be calculated because of the excessive amount of computing time needed. Therefore, a new algorithm LigPath for approximate calculation of a ligand’s pathway into the binding pocket has been developed. This new algorithm is based on a linkage of directional guiding of the ligand, Monte-Carlo-Search and minimization. In order to evaluate the performance of the algorithm, the guinea-pig histamine H₁ receptor was investigated in combination with one of its potent agonists, histaprodifen, which is proposed to bind in a pocket deep between the transmembrane helices of the receptor. Our calculations show that the amino acids Tyr194, Phe193, Phe436 and Phe433 guide the positively charged histaprodifen from the extracellular part of the receptor into the binding pocket.