Nonlinear machine learning in simulations of soft and biological materials

Abstract

Interpretable parameterisations of free energy landscapes for soft and biological materials calculated from molecular simulation require the availability of ‘good’ collective variables (CVs) capable of discriminating the metastable states of the system and the barriers between them. If these CVs are coincident with the slow collective modes governing the long-time dynamical evolution, then they also furnish good coordinates in which to perform enhanced sampling to surmount high free energy barriers and efficiently explore and recover the landscape. Non-linear manifold learning techniques provide a means to systematically extract such CVs from molecular simulation trajectories by identifying and extracting low-dimensional manifolds lying latent within the high-dimensional coordinate space. We survey recent advances in data-driven CV discovery and enhanced sampling using non-linear manifold learning, describe the mathematical and theoretical underpinnings of these techniques, and present illustrative examples to molecular folding and colloidal self-assembly. We close with our outlook and perspective on future advances in this rapidly evolving field.     

Conformational Requirements of Acetylcholine Analogues and Local Anaesthetics

ATTEMPTS have been made to view the roles of acetylcholine and of cholinergic agonists as triggering permeability changes in excitable membranes through attachment to acetylcholine receptor biopolymers^1,2. Similarly, it has been proposed that local anaesthetics might block nerve conduction through attachment to axonal acetylcholine receptors^3,4. These considerations raise a number of questions. Are certain specific conformations essential for molecules related to acetylcholine either to “trigger” or to “block” depolarization of excitable membranes ? Are the conformations of such molecules identical in the crystal and in solution ? What are the rotational barriers to conformational alteration of such molecules ?     

Laser impact assessment in a biofilm-forming bacterium Pseudoalteromonas carrageenovora using a flow cytometric system

Impact by pulsed laser irradiations from an Nd:YAG laser on the marine biofilm-forming bacterium Pseudoalteromonas carrageenovora has been studied using a flow cytometric system. The biofilm-forming bacteria in the planktonic state have been irradiated while flowing, and the mortality and bacterial attachment have been determined by exposing TiN coupons in the system. Coupons suspended in the non-irradiated bacterial flow were treated as the control. The fluence used in the study was 0.1 J/cm(2). Three flow rates (14, 28, and 42 cm/min) and two exposure durations (15 and 30 min) were tested. The results showed the increase in bacterial mortality with the decrease in flow rate. The maximum mortality of 27.5% was observed when the flow rate was 14 cm/min. The bacterial attachment increased with the increase in flow rate and exposure duration. The area of bacterial attachment on the experimental coupons exposed to the irradiated sample was significantly lesser than that for the nonirradiated sample. The results thus show in a flowing system, low power pulsed laser irradiations could reduce the bacterial attachment even though it did not cause significant mortality.     

Reproductive isolation mechanisms among four closely-related species of Conospermum (Proteaceae)

The effectiveness of geographical isolation, ecological isolation, temporal isolation, mechanical isolation, ethological isolation, cross-incompatibility, hybrid inviability, hybrid sterility and hybrid breakdown as practical barriers to gene flow in the field between Conospermum taxifolium, C. ericifolium, C. ellipticum and C. longifolium has been quantified. The barriers to gene flow between C. ericifolium and C. ellipticum are completely effective, owing to their allopatric distributions. The barriers to gene flow between C. taxifolium and these two species are only partially effective, as their ecological separation breaks down in intermediate habitats, and partially-fertile F₁ plants can grow in the areas of overlap. The barriers to gene flow between C. longifolium and the other three species are almost completely effective, as cross-incompatibility is very high and the F₁ plants are female-sterile.     

Flow modelling within a scaffold under the influence of uni-axial and bi-axial bioreactor rotation

The problem of donor scarcity has led to the recent development of tissue engineering technologies, which aim to create implantable tissue equivalents for clinical transplantation. These replacement tissues are being realised through the use of biodegradable polymer scaffolds; temporary/permanent substrates, which facilitate cell attachment, proliferation, retention and differentiated tissue function. To optimise gas transfer and nutrient delivery, as well as to mimic the fluid dynamic environment present within the body, a dynamic system might be chosen. Experiments have shown that dynamic systems enhance tissue growth, with the aid of scaffolds, as compared to static culture systems. Very often, tissue growth within scaffolds is only seen to occur at the periphery. The present study utilises the Computational Fluid Dynamics package FLUENT, to provide a better understanding of the flow phenomena in scaffolds, within our novel bioreactor system. The uni-axial and bi-axial rotational schemes are studied and compared, based on a vessel rotating speed of 35 rpm. The wall shear stresses within and without the constructs are also studied. Findings show that bi-axial rotation of the vessel results in manifold increases of fluid velocity within the constructs, relative to uni-axial rotation about the X- and Z-axes, respectively.     

Intrinsic incompatibilities evolving as a by‐product of divergent ecological selection: Considering them in empirical studies on divergence with gene flow

The possibility of intrinsic barriers to gene flow is often neglected in empirical research on local adaptation and speciation with gene flow, for example when interpreting patterns observed in genome scans. However, we draw attention to the fact that, even with gene flow, divergent ecological selection may generate intrinsic barriers involving both ecologically selected and other interacting loci. Mechanistically, the link between the two types of barriers may be generated by genes that have multiple functions (i.e., pleiotropy), and/or by gene interaction networks. Because most genes function in complex networks, and their evolution is not independent of other genes, changes evolving in response to ecological selection can generate intrinsic barriers as a by‐product. A crucial question is to what extent such by‐product barriers contribute to divergence and speciation—that is whether they stably reduce gene flow. We discuss under which conditions by‐product barriers may increase isolation. However, we also highlight that, depending on the conditions (e.g., the amount of gene flow and the strength of selection acting on the intrinsic vs. the ecological barrier component), the intrinsic incompatibility may actually destabilize barriers to gene flow. In practice, intrinsic barriers generated as a by‐product of divergent ecological selection may generate peaks in genome scans that cannot easily be interpreted. We argue that empirical studies on divergence with gene flow should consider the possibility of both ecological and intrinsic barriers. Future progress will likely come from work combining population genomic studies, experiments quantifying fitness and molecular studies on protein function and interactions.     

Mating system as a barrier to gene flow

Understanding mating system as one of reproductive isolating barriers remains important although this barrier is classified in a different sense from behavioral, ecological, and mechanical isolating barriers. Selfing enhances incipient speciation while outcrossing facilitates species integrity. Here, I study how mating system affects gene exchanges between genetically diverging species in a hybrid zone. Results show that a predominant selfing species has a greater barrier to selective gene flow than does a predominant outcrossing species. Barrier to neutral gene flow convexly changes with the selfing rate due to linkage disequilibrium, with a maximum at around intermediate selfing rate. Asymmetric transient or steady‐state barriers to neutral gene flow occur between two sides of a hybrid zone when the neutral gene is affected by its linked selective gene whose alternative alleles are adaptive to heterogeneous habitats. Selfing interacts with both a physical barrier and a density‐dependent ecological regulation (a logarithmic model) to strengthen the barriers to neutral and selective gene flow. This theory helps to interpret incipient speciation driven by selfing or to explain the asymmetric gene flow or unequal genomic mixtures between closely related species caused by their asymmetric mating systems in natural hybrid zones.     

沼蛤(Limnoperna fortunei)幼虫的附着行为特性

沼蛤(Limnoperna fortunei Dunker,1857),俗称淡水壳菜,是一种扩散能力与适应能力都较强的入侵性底栖动物,它对自然环境与输水工程的侵入和大规模附着,不仅会破坏当地的生物群落结构,而且沼蛤成贝在工程内稳定附着后难以去除,造成重大工程危害。通过试验研究沼蛤幼虫的附着行为特性,并利用该特性对原水中的幼虫进行吸引附着处理,以减少幼虫进入工程造成污损附着。选用前期研究推荐的沼蛤幼虫喜好附着的黄麻材料制成的附着排作为试验材料,设置5组附着排长度工况:1,3,5,6,8 m,在5组流量工况:3.1,5.7,6.7,9.6,12.1 L/s下开展试验,研究不同附着排长度和流量条件下沼蛤幼虫的附着行为,以便优选出吸附幼虫的最佳条件。试验结果表明:(1)黄麻材料的吸附效果与附着排长度呈正相关关系,材料长度为3—5m时,吸附率即可达到50%;材料长度为6—8 m时,平均效果为62—76%,最佳吸附率可达93%;(2)流量过大会降低幼虫吸附效果,吸附也更不稳定;(3)幼虫发育先后经历D型幼虫、前期壳顶幼虫、后期壳顶幼虫、踯行期4个时期,吸附材料对后期壳顶和踯行期幼虫的吸附效果较前期壳顶幼虫更好;(4)附着材料密集布置于较短的长度内比稀疏布置于较长的长度内更有利于提高附着效果。     

Monolithic bioreactors: Effect of chymotrypsin immobilization on its biocatalytic properties

The effect of different modes of α-chymotrypsin attachment to the surface of methacrylate-based ultrashort monolithic minicolumns on enzyme activity has been studied. The immobilization of protease was carried out via direct covalent binding of chymotrypsin, as well as via its attachment through small and polymer spacers. It was established that the lowest enzyme activity against N-benzoyl-l-tyrosine ethyl ester was found for bioreactor obtained via direct attachment of chymotrypsin to the surface of GMA–EDMA minidisks, whereas the highest parameter close to that determined for dissolved enzyme was found in the case of bioreactor prepared by the introduction of copolymer of 2-deoxy-N-methacryloylamido-d-glucose with N-vinylpyrrolidone and acrolein as a long and flexible polymer spacer. Additionally, the effect of flow rate of substrate recirculation on bioconversion efficiency was examined. Independently on immobilization method, the increase of flow rate led to the raise of biocatalytic efficiency.     

Rate enhancement by guided diffusion. Chain length dependence of repressor-operator association rates

Association rates are calculated for cases where one reaction partner belongs to a chain that has an unspecific affinity to the other. Provided that the unspecific attachment does not completely suppress diffusion along the chain, this channeling may considerably speed up the association. Explicit formulae are derived to show how this effect depends on the chain length and other parameters. The influence of electrostatic forces and reaction barriers is discussed. Time dependent solutions of the diffusion equations are analyzed in order to test the usual steady state assumptions. Experiments on the repressor-operator system seem to be in good agreement with our theory.     

Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep

The rapid expansion of road networks has reduced connectivity among populations of flora and fauna. The resulting isolation is assumed to increase population extinction rates, in part because of the loss of genetic diversity. However, there are few cases where loss of genetic diversity has been linked directly to roads or other barriers. We analysed the effects of such barriers on connectivity and genetic diversity of 27 populations of Ovis canadensis nelsoni (desert bighorn sheep). We used partial Mantel tests, multiple linear regression and coalescent simulations to infer changes in gene flow and diversity of nuclear and mitochondrial DNA markers. Our findings link a rapid reduction in genetic diversity (up to 15%) to as few as 40 years of anthropogenic isolation. Interstate highways, canals and developed areas, where present, have apparently eliminated gene flow. These results suggest that anthropogenic barriers constitute a severe threat to the persistence of naturally fragmented populations.     

Post-pollination barriers do not explain the persistence of two distinct Antirrhinum subspecies with parapatric distribution

Empirical studies of post-pollination barriers to gene flow between recently diverged plant species are important to understand ecological processes underlying speciation. Using greenhouse and common garden experiments, we investigated the strength of post-pollination barriers that restrict or prevent gene flow between two subspecies of Antirrhinum: Antirrhinum majus pseudomajus and A. m. striatum. The two are distributed parapatrically but share the same major pollinators (bumblebees), and form narrow hybrid zone in many areas of southern France and northern Spain where they come into close contact. We assessed the strength and symmetry of mating barriers and their homogeneity among populations by comparing fruit set, seed set and offspring performances between intra- and inter-subspecific crosses performed in parental and hybrid populations. Although all populations showed high levels of self-incompatibility, we found very little evidence for barriers to gene flow once pollen had been transferred to the stigma. We suggest that reproductive isolation in this system mostly involves barriers related to processes occurring before pollination, with little or no role of post-pollination barriers.     

Flow injection analysis-based methodology for automatic on-line monitoring and quality control for biodiesel production

An automated on-line approach based on determination of free and bound glycerol was here proposed to monitor biodiesel production. The method was based on liquid-liquid extraction of glycerol from the biodiesel to an aqueous ethanolic phase in which glycerol is oxidized to formaldehyde with meta periodate with subsequent reaction with acetylacetone. The reaction product was photometrically measured at 410 nm. Free and bound glycerol were differentiated by glycerides hydrolysis with potassium ethylate. The experimental set-up consisted of a flow-injection manifold for liquid-liquid extraction without phase separation and iterative change of the flow direction that enabled: (a) filling the flow manifold with a meta periodate-acetylacetone acceptor phase; (b) sampling of small amounts (microl) from the reactor; (c) determination of free glycerol by extraction from biodiesel to the aqueous phase with simultaneous oxidation-reaction with acetylacetone in the acceptor phase; (d) continuous monitoring of the aqueous phase by passage through a photometric detector; (e) filling the flow manifold with a potassium ethylate-meta periodate-acetylacetone new acceptor phase; (d) repetition of steps b-to-d to determine total glycerol after saponification of the bound glycerol by potassium ethylate; and (f) determination of bound glycerol by difference between the second and first analyses. The results showed that the proposed automated on-line method is a suitable option in routine analysis during biodiesel production.     

Fertility depression among cheese‐making Penicillium roqueforti strains suggests degeneration during domestication

Genetic differentiation occurs when gene flow is prevented, due to reproductive barriers or asexuality. Investigating the early barriers to gene flow is important for understanding the process of speciation. Here, we therefore investigated reproductive isolation between different genetic clusters of the fungus Penicillium roqueforti, used for maturing blue cheeses, and also occurring as food spoiler or in silage. We investigated premating and postmating fertility between and within three genetic clusters (two from cheese and one from other substrates), and we observed sexual structures under scanning electron microscopy. All intercluster types of crosses showed some fertility, suggesting that no intersterility has evolved between domesticated and wild populations despite adaptation to different environments and lack of gene flow. However, much lower fertility was found in crosses within the cheese clusters than within the noncheese cluster, suggesting reduced fertility of cheese strains, which may constitute a barrier to gene flow. Such degeneration may be due to bottlenecks during domestication and/or to the exclusive clonal replication of the strains in industry. This study shows that degeneration has occurred rapidly and independently in two lineages of a domesticated species. Altogether, these results inform on the processes and tempo of degeneration and speciation.     

Landscape composition modulates population genetic structure of Eriosoma lanigerum (Hausmann) on Malus domestica Borkh in central Chile

Landscape genetics have been particularly relevant when assessing the influence of landscape characteristics on the genetic variability and the identification of barriers to gene flow. Linking current practices of area-wide pest management information on pest population genetics and geographical barriers would increase the efficiency of these programs. The woolly apple aphid, Eriosoma lanigerum (Hausmann), an important pest of apple orchards worldwide, was collected on apple trees (Malus domestica Borkh) from different locations in a 400 km north-south transect trough central Chile. In order to determine if there was population structure, diversity and flow were assessed. A total of 215 individuals from these locations were analysed using Inter Simple Sequence Repeat (ISSR) markers. Four ISSR primers generated a total of 114 polymorphic loci. The percentage of molecular variation among locations was 18%. As the algorithm used by structure may be poorly suited for inferring the number of genetic clusters in a data set that has an IBD relationship, the number of genetic clusters in the samples was also analyzed using a Bayesian clustering method implemented in software Baps version 4.14. We inferred the presence of four genetic clusters in the study region. Clustering of individuals followed a pattern explained by some geographical barriers. Using partial Mantel tests, we detected barriers to gene flow other than distance, created by a combination of main rivers and mountains. Although landscape genetics are rarely used in pest management, our results suggest that these tools may be suitable for the design of area-wide pest management programs.     

Current geography masks dynamic history of gene flow during speciation in northern Australian birds

Genome divergence is greatly influenced by gene flow during early stages of speciation. As populations differentiate, geographic barriers can constrain gene flow and so affect the dynamics of divergence and speciation. Current geography, specifically disjunction and continuity of ranges, is often used to predict the historical gene flow during the divergence process. We test this prediction in eight meliphagoid bird species complexes codistributed in four regions. These regions are separated by known biogeographical barriers across northern Australia and Papua New Guinea. We find that bird populations currently separated by terrestrial habitat barriers within Australia and marine barriers between Australia and Papua New Guinea have a range of divergence levels and probability of gene flow not associated with current range connectivity. Instead, geographic distance and historical range connectivity better predict divergence and probability of gene flow. In this dynamic environmental context, we also find support for a nonlinear decrease of the probability of gene flow during the divergence process. The probability of gene flow initially decreases gradually after a certain level of divergence is reached. Its decrease then accelerates until the probability is close to zero. This implies that although geographic connectivity may have more of an effect early in speciation, other factors associated with higher divergence may play a more important role in influencing gene flow midway through and later in speciation. Current geographic connectivity may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation.     

Role of outer membrane c-type cytochromes MtrC and OmcA in Shewanella oneidensis MR-1 cell production, accumulation, and detachment during respiration on hematite

The iron-reducing bacterium Shewanella oneidensis MR-1 has the capacity to contribute to iron cycling over the long term by respiring on crystalline iron oxides such as hematite when poorly crystalline phases are depleted. The ability of outer membrane cytochromes OmcA and MtrC of MR-1 to bind to and transfer electrons to hematite has led to the suggestion that they function as terminal reductases when this mineral is used as a respiratory substrate. Differences in their redox behavior and hematite-binding properties, however, indicate that they play different roles in the electron transfer reaction. Here, we investigated how these differences in cytochrome behavior with respect to hematite affected biofilm development when the mineral served as terminal electron acceptor (TEA). Upon attachment to hematite, cells of the wild-type (WT) strain as well as those of a ΔomcA mutant but not those of a ΔmtrC mutant replicated and accumulated on the mineral surface. The results indicate that MtrC but not OmcA is required for growth when this mineral serves as TEA. While an OmcA deficiency did not impede cell replication and accumulation on hematite prior to achievement of a maximum surface cell density comparable to that established by WT cells, OmcA was required for efficient electron transfer and cell attachment to hematite once maximum surface cell density was achieved. OmcA may therefore play a role in overcoming barriers to electron transfer and cell attachment to hematite imposed by reductive dissolution of the mineral surface from cell respiration associated with achievement of high surface cell densities.     

Molecular Markers Reveal Limited Population Genetic Structure in a North American Corvid,Clark’s Nutcracker (Nucifraga columbiana)

The genetic impact of barriers and Pleistocene glaciations on high latitude resident species has not been widely investigated. The Clark’s nutcracker is an endemic North American corvid closely associated with Pinus-dominated forests. The nutcracker’s encompasses known barriers to dispersal for other species, and glaciated and unglaciated areas. Clark’s nutcrackers also irruptively disperse long distances in search of pine seed crops, creating the potential for gene flow among populations. Using the highly variable mitochondrial DNA control region, seven microsatellite loci, and species distribution modeling, we examined the effects of glaciations and dispersal barriers on population genetic patterns and population structure of nutcrackers. We sequenced 900 bp of mitochondrial control region for 169 individuals from 15 populations and analysed seven polymorphic microsatellite loci for 13 populations across the Clark’s nutcracker range. We used species distribution modeling and a range of phylogeographic analyses to examine evolutionary history. Clark’s nutcracker populations are not highly differentiated throughout their range, suggesting high levels of gene flow among populations, though we did find some evidence of isolation by distance and peripheral isolation. Our analyses suggested expansion from a single refugium after the last glacial maximum, but patterns of genetic diversity and paleodistribution modeling of suitable habitat were inconclusive as to the location of this refugium. Potential barriers to dispersal (e.g. mountain ranges) do not appear to restrict gene flow in Clark’s nutcracker, and postglacial expansion likely occurred quickly from a single refugium located south of the ice sheets.     

Making use of the social network in conservation genomics: Integrating kinship and network analyses to understand connectivity

Inferring and quantifying recent barriers to connectivity is increasingly important for conservation and management in a world undergoing rapid environmental change. Traditional measures of genetic differentiation can take many generations to reflect a new barrier to connectivity. Although methods that use the linkage disequilibrium signal in mixed genetic samples are able to reflect recent levels of gene flow, they are not suitable for use in situations with low levels of genetic differentiation. Kinship‐based methods, those that assess the spatio‐temporal distribution of related individuals, have been used in this context, but a formal statistical framework for such approaches has been lacking. In this issue of Molecular Ecology Resources, Escoda, et al. adapt the assortativity coefficient, AC, to analyse the networks of kin relationships in the Pyrenean desman (Galemys pyrenaicus) across potential barriers to dispersal. Their modified AC quantifies the proportion of missing kin relationships across putative dispersal barriers with respect to the expected proportion if there was no barrier. This application highlights that AC can be used to test the null hypothesis that a putative barrier has no effect on gene flow, in which case AC is not significantly different from 0. The method represents a useful step forward in conservation genomics by developing and adapting tools to assess contemporary connectivity using genomic data.