An Interatomic Potential Model for H2O: Applications to Water and Ice Polymorphs

Abstract

A new interatomic potential model for H₂O which consists of 2-body central (O-H, O-O and H-H) and 3-body teams and does not contain artificial constraints on the motions of oxygen and hydrogen atoms is proposed. The interatomic potential function parameters were determined empirically so as to reproduce the fundamental and essential features of water and ice Ih using molecular dynamics (MD) methods.

We carried out the MD simulations of water, and find the Ice Ih, Ice II and Ice IX using this potential model, in structures and physical properties are in agreement with the experimental results except for the compressibilities of both water and ice Ih. We expect that, by refining this model, we can apply this model to problems involving the reaction of water molecules with other components.     

Phylogeographic analysis of North American populations of the parasitic herbaceous plant Monotropa hypopitys L. reveals a complex history of range expansion from multiple late glacial refugia

Aim We carried out a phylogeographic study across the range of the herbaceous plant species Monotropa hypopitys L. in North America to determine whether its current disjunct distribution is due to recolonization from separate eastern and western refugia after the Last Glacial Maximum (LGM). Location North America: Pacific Northwest and north‐eastern USA/south‐eastern Canada. Methods Palaeodistribution modelling was carried out to determine suitable climatic regions for M. hypopitys at the LGM. We analysed between 155 and 176 individuals from 39 locations spanning the species’ entire range in North America. Sequence data were obtained for the chloroplast rps2 gene (n = 168) and for the nuclear ITS region (n = 158). Individuals were also genotyped for eight microsatellite loci (n = 176). Interpolation of diversity values was used to visualize the range‐wide distribution of genetic diversity for each of the three marker classes. Minimum spanning networks were constructed showing the relationships between the rps2 and ITS haplotypes, and the geographical distributions of these haplotypes were plotted. The numbers of genetic clusters based on the microsatellite data were estimated using Bayesian clustering approaches. Results The palaeodistribution modelling indicated suitable climate envelopes for M. hypopitys at the LGM in both the Pacific Northwest and south‐eastern USA. High levels of genetic diversity and endemic haplotypes were found in Oregon, the Alexander Archipelago, Wisconsin, and in the south‐eastern part of the species’ distribution range. Main conclusions Our results suggest a complex recolonization history for M. hypopitys in North America, involving persistence in separate eastern and western refugia. A generally high degree of congruence between the different marker classes analysed indicated the presence of multiple refugia, with at least two refugia in each area. In the west, putative refugia were identified in Oregon and the Alexander Archipelago, whereas eastern refugia may have been located in the southern part of the species’ current distribution, as well as in the ‘Driftless Area’. These findings are in contrast to a previous study on the related species Orthilia secunda, which has a similar disjunct distribution to M. hypopitys, but which appears to have recolonized solely from western refugia.     

Influence of larval outbreaks on the climate reconstruction potential of an Arctic shrub

Arctic shrubs have a strong potential for climate and environmental reconstructions in the chronically understudied regions of the high northern latitudes. The climate dynamics of these regions are important to understand because of large-scale feedbacks to the global climate system. However, little is known about other factors influencing shrub ring growth, possibly obscuring their climate signal. For example, as of yet we are not able to differentiate between herbivory or climatically induced growth depressions. Here, we use one of the most common Arctic shrubs, Alnus viridis as a test case to address this question. We sampled Alnus in Kobbefjord, Greenland, measured shrub-ring width and cell wall thickness and built site chronologies of each parameter. We analysed climate-growth relationships, tested their stability over time and employed a pointer-year analysis to detect growth depressions. We employed bootstrapped transfer function stability tests (BTFS) to assess the suitability of our shrub chronologies for climate reconstruction. Correlations with climate data showed strong significantly positive and stable correlations between summer temperature and ring-width with the exception of the recent decade. A climate reconstruction model failed stability tests, when the complete period of record was used for calibration and verification. Wood anatomy analysis uncovered the occurrence of unusual cell structure (very thin cell walls) in the exceptionally narrow ring of 2004, a recorded insect outbreak year in other parts of Greenland. When excluding the affected ring and a recovery period, the reconstruction model passed all tests, suggesting that the unusual 2004 ring was not climate driven, but rather the result of an insect attack. When combining anatomical analysis with traditional ring-width measurements, we move a step further in potentially distinguishing small rings caused by insect attacks from small rings formed in climatically challenging years. While this study does not provide unambiguous evidence, it does provide potential useful methodological combinations to enable more robust climate reconstructions in areas where climatic records are extremely sparse.     

Ice‐‐bacteria as antagonists in biological frost protection

Investigated was the efficacy of 4 ice nucleation‐inactive (ice^‐) bacterial strains (A506, GSPB 1147, 1181, 2357) at 4 ice nucleation active (ice⁺) strains (553, 554, GSPB 1139, 2035) on the surface of 4 culture crops (corn, tomato, bush‐ and field bean). Examinated was the reduction of frost damage at the used culture crops by inoculation with ice⁺ and ice^‐ strains at 4 different variants (A‐D) under laboratory conditions. The ice nucleation activity was determined by the tube‐freezing‐assay. An effective reduction of ice⁺ bacteria was possible, when plant surfaces were preinoculated (3days) with ice^‐bacteria before ice⁺ bacterial strains colonized the surfaces of plants. A statistical comparison of mean values of obtained results showed, the ice crystallization (INT) by inoculation started at ‐3°C and in mean (MNT) below ‐5°C independent of the used ice⁺ and ice^‐ strains. Obtained differences were not significant. As untreated as colonized plants with antagonists started to freeze at ‐5 and ‐6°C and in average at ‐7°C. However, the preinoculation resulted in 1.38 K differences for the temperatures, at which 50% of leaves were frozen (PROZ 50) in favour of preinoculated plants. This difference in freeze temperatures by preinoculation with ice^‐ bacteria was discussed as a possible method of frost protection.     

The colonization of Scottish islands by the common shrew, Sorex araneus (Eulipotyphla: Soricidae)

In this paper we apply molecular methods to study the colonization of islands off the west coast of Scotland by the common shrew ( Sorex araneus L.), and current gene flow. We collected 497 individuals from 13 islands of the Inner Hebrides and Clyde Island groups and six mainland regions. Individuals were genotyped at eight microsatellite loci, and the mitochondrial cytochrome b sequence (1140 base pairs) was obtained for five individuals from each island/mainland region. Based on these molecular data, island colonization apparently proceeded directly from the mainland, except for Islay, for which Jura was the most likely source population. Raasay may also have been colonized by island hopping. Most island populations are genetically very distinct from the mainland populations, suggesting long periods of isolation. Two exceptions to this are the islands of Skye and Seil, which are geographically and genetically close to the mainland, suggesting in each case that there has been long-term gene flow between these islands and the mainland. We consider possible methods of island colonization, including human-mediated movement, swimming, and land and ice bridges.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 797–808.     

Ringed seal (Pusa hispida) tooth annuli as an index of reproduction in the Beaufort Sea

Multi-decadal time-series of biological indices that reflect the state of a population are rare in ecological studies, but invaluable for assessing environmental regulation of population dynamics. We utilized canine teeth extracted from ringed seals (Pusa hispida) killed by polar bears (Ursus maritimus) in the Beaufort Sea, Canada, in 1985–2011, to obtain widths of annual growth layers in the cementum. Canine teeth for 75 individuals were measured and compared across years using a proportional width index (PWI) spanning 1965–2007. PWI was positively correlated with ringed seal ovulation rate obtained independently from other studies and was significantly lower than normal during ringed seal reproductive declines in 1974–75, 1984–87, 1991–93, and 2004–05, suggesting that PWI reflects ringed seal reproductive capacity. The PWI was also examined against climatic and sea ice factors to assess environmental regulation of ringed seal reproduction. Results suggest that ringed seals benefit from cyclonic circulation regimes in the Beaufort Sea, and an earlier breakup of sea ice in summer that may positively influence the quality and quantity of food during the open water season. Results highlight how cementum annuli in the canine teeth of ringed seals can provide an index of body state and linkages to sea ice conditions. Canine teeth from ringed seals can function as a means to monitor the effects of past Arctic marine variability on area-specific populations for which there are few independent empirical data.     

Pursuit of proteomic excellence and the excitement in Košice,Slovakia, at the 11th Central and Eastern European Proteomic Conference (CEEPC)

The Central and Eastern European Proteomic Conference (CEEPC) successfully launched its second decade of proteomics in Ko?ice, Slovakia with a program of systems biology, cellular, clinical, veterinary and sports proteomics. Whilst many conferences are struggling to attract participants, CEEPC with its outstanding track record and unique ‘family – feel’ packaged with excellent ambiance is thriving and bringing together proteomics experts from academia, industry, scientific specialties, clinics and precision medicine communities interested in resolving mysteries about protein functionalities in health and disease. CEEPC is also renowned for addressing humanitarian global healthcare issues, may it be ageing, chronic diseases or global epidemics. This year CEEPC intertwined with Ko?ice Peace Marathon’s pursuit of excellence in sports and initiatives including sports medicine and global peace.     

Mechanisms underlying insect freeze tolerance

Freeze tolerance – the ability to survive internal ice formation – has evolved repeatedly in insects, facilitating survival in environments with low temperatures and/or high risk of freezing. Surviving internal ice formation poses several challenges because freezing can cause cellular dehydration and mechanical damage, and restricts the opportunity to metabolise and respond to environmental challenges. While freeze‐tolerant insects accumulate many potentially protective molecules, there is no apparent ‘magic bullet’ – a molecule or class of molecules that appears to be necessary or sufficient to support this cold‐tolerance strategy. In addition, the mechanisms underlying freeze tolerance have been minimally explored. Herein, we frame freeze tolerance as the ability to survive a process: freeze‐tolerant insects must withstand the challenges associated with cooling (low temperatures), freezing (internal ice formation), and thawing. To do so, we hypothesise that freeze‐tolerant insects control the quality and quantity of ice, prevent or repair damage to cells and macromolecules, manage biochemical processes while frozen/thawing, and restore physiological processes post‐thaw. Many of the molecules that can facilitate freeze tolerance are also accumulated by other cold‐ and desiccation‐tolerant insects. We suggest that, when freezing offered a physiological advantage, freeze tolerance evolved in insects that were already adapted to low temperatures or desiccation, or in insects that could withstand small amounts of internal ice formation. Although freeze tolerance is a complex cold‐tolerance strategy that has evolved multiple times, we suggest that a process‐focused approach (in combination with appropriate techniques and model organisms) will facilitate hypothesis‐driven research to understand better how insects survive internal ice formation.     

Functional impairment of MSC induced by transient warming events: Correlation with loss of adhesion and altered cell size

Background

We recently showed that transient warming effects decreased the functional and adhesion properties of mesenchymal stromal cells (MSC) while post-thaw viability remained high. In an attempt to better predict functional impairment of cryopreserved MSC, we further analysed the correlation between viability, immunosuppressive activity and adhesion of cells exposed or not to warming events.

Prokaryotes in the WAIS Divide ice core reflect source and transport changes between Last Glacial Maximum and the early Holocene

We present the first long‐term, highly resolved prokaryotic cell concentration record obtained from a polar ice core. This record, obtained from the West Antarctic Ice Sheet (WAIS) Divide (WD) ice core, spanned from the Last Glacial Maximum (LGM) to the early Holocene (EH) and showed distinct fluctuations in prokaryotic cell concentration coincident with major climatic states. The time series also revealed a ~1,500‐year periodicity with greater amplitude during the Last Deglaciation (LDG). Higher prokaryotic cell concentration and lower variability occurred during the LGM and EH than during the LDG. A sevenfold decrease in prokaryotic cell concentration coincided with the LGM/LDG transition and the global 19 ka meltwater pulse. Statistical models revealed significant relationships between the prokaryotic cell record and tracers of both marine (sea‐salt sodium [ssNa]) and burning emissions (black carbon [BC]). Collectively, these models, together with visual observations and methanosulfidic acid (MSA) measurements, indicated that the temporal variability in concentration of airborne prokaryotic cells reflected changes in marine/sea‐ice regional environments of the WAIS. Our data revealed that variations in source and transport were the most likely processes producing the significant temporal variations in WD prokaryotic cell concentrations. This record provided strong evidence that airborne prokaryotic cell deposition differed during the LGM, LDG, and EH, and that these changes in cell densities could be explained by different environmental conditions during each of these climatic periods. Our observations provide the first ice‐core time series evidence for a prokaryotic response to long‐term climatic and environmental processes.