Ethanol from sugarcane in Brazil: a ‘midway’ strategy for increasing ethanol production while maximizing environmental benefits

This article reviews the history and current state of ethanol production from sugarcane in Brazil and presents a strategy for improving ecosystem services and production. We propose that it is possible to produce ethanol from sugarcane while maintaining or even recovering some of Brazil's unique neotropical biodiversity and ecosystem climate services. This approach to the future of sustainable and responsible ethanol production is termed the ‘midway’ strategy. The ‘midway’ strategy involves producing the necessary biotechnology to increase productivity while synergistically protecting and regenerating rainforest. Three main areas of scientific and technological advance that are key to realizing the ‘midway’ strategy are: (i) improving the quality of scientific data on sugarcane biology as pertains to its use as a bioenergy crop; (ii) developing technologies for the use of bagasse for cellulosic ethanol; and (iii) developing policies to improve the ecosystem services associated with sugarcane landscapes. This article discusses these three issues in the general context of biofuels production and highlights examples of scientific achievements that are already leading towards the ‘midway’ strategy.     

Biotechnology,Big Data and Artificial Intelligence

Developments in biotechnology are increasingly dependent on the extensive use of big data, generated by modern high‐throughput instrumentation technologies, and stored in thousands of databases, public and private. Future developments in this area depend, critically, on the ability of biotechnology researchers to master the skills required to effectively integrate their own contributions with the large amounts of information available in these databases. This article offers a perspective of the relations that exist between the fields of big data and biotechnology, including the related technologies of artificial intelligence and machine learning and describes how data integration, data exploitation, and process optimization correspond to three essential steps in any future biotechnology project. The article also lists a number of application areas where the ability to use big data will become a key factor, including drug discovery, drug recycling, drug safety, functional and structural genomics, proteomics, pharmacogenetics, and pharmacogenomics, among others.     

Modelling emotion,perfecting heart: disassembling technologies of affect with an android bodhisattva in Japan

As part of a surge in technologies with so-called ‘artificial emotional intelligence’, robotics engineers and Buddhist monks in Japan have developed an android bodhisattva to deliver teachings at a popular Zen temple. Like many recent robots in Japan, the android is designed to impact visitors’ feelings. For this reason, it can be called a ‘technology of affect’. In order to communicate how new affective technologies are facilitating intimacy in human-machine relations in Japan, we employ the concept of ‘disassembling’. By conceptually disassembling technologies of affect and placing them in performative contexts, we show how technologies of affect also disassemble established associations between artificial agents and the feelings they evoke in popular imaginaries. We argue that identifying these disassembling processes helps demonstrate how emerging AI technologies can engender social change at the level of affect through evocative depictions of machine emotion.     

Niche partitioning and the effect of interspecific competition on microhabitat use by two sympatric galaxiid stream fishes

1. Numerous interacting abiotic and biotic factors influence niche use and assemblage structure of freshwater fishes, but the strength of each factor changes with spatial scale. Few studies have examined the role of interspecific competition in structuring stream fish assemblages across spatial scales. We used field and laboratory approaches to examine microhabitat partitioning and the effect of interspecific competition on microhabitat use in two sympatric stream fishes (Galaxias‘southern’ and Galaxias gollumoides) at large (among streams and among sites within streams) and small (within artificial stream channels) spatial scales. 2. Diurnal microhabitat partitioning and interspecific competition at large spatial scales were analysed among three sympatry streams (streams with allotopic and syntopic sites; three separate catchments) and four allopatry streams (streams with only allotopic sites; two separate catchments). Electro‐fishing was used to sample habitat use of fishes at 30 random points within each site by quantifying four variables for each individual: water velocity, depth, distance to nearest cover and substratum size. Habitat availability was then quantified for each site by measuring those variables at each of 50 random points. Diet and stable isotope partitioning was analysed from syntopic sites only. Diel cycles of microhabitat use and interspecific competition at small spatial scales were examined by monitoring water velocity use over 48 h in artificial stream channels for three treatments: (i) allopatric G. ‘southern’ (10 G. ‘southern’); (ii) allopatric G. gollumoides (10 G. gollumoides) and (iii) sympatry (five individuals of each species). 3. One hundred and ninety‐four G. ‘southern’ and 239 G. gollumoides were sampled across all seven streams, and habitat availability between the two species was similar among all sites. Galaxias‘southern’ utilised faster water velocities than G. gollumoides in both the field and in channel experiments. Both species utilised faster water velocities in channels at night than during the day. Diet differences were observed and were supported by isotopic differences (two of three sites). No interspecific differences were observed for the other three microhabitat variables in the field, and multivariate habitat selection did not differ between species. Interspecific competition had no effect on microhabitat use of either species against any variable either in the field (large scale) or in channels (small scale). 4. The results suggest that niche partitioning occurs along a subset of microhabitat variables (water velocity use and diet). Interspecific competition does not appear to be a major biotic factor controlling microhabitat use by these sympatric taxa at any spatial scale. The results further suggest that stream fish assemblages are not primarily structured by biotic factors, reinforcing other studies de‐emphasising interspecific competition.     

Artificial intelligence for microbial biotechnology: beyond the hype

It has been a landmark year for artificial intelligence (AI) and biotechnology. Perhaps the most noteworthy of these advances was Google DeepMind’s AlphaFold2 algorithm which smashed records in protein structure prediction (Jumper et al., 2021, Nature, 596, 583) complemented by progress made by other research groups around the globe (Baek et al., 2021, Science, 373, 871; Zheng et al., 2021, Proteins). For the first time in history, AI achieved protein structure models rivalling the accuracy of experimentally determined structures. The power of accurate protein structure prediction at our fingertips has countless implications for drug discovery, de novo protein design and fundamental research in chemical biology. While acknowledging the significance of these breakthroughs, this perspective aims to cut through the hype and examine some key limitations using AlphaFold2 as a lens to consider the broader implications of AI for microbial biotechnology for the next 15 years and beyond.     

The urban matrix and artificial light restricts the nightly ranging behaviour of Gould's long‐eared bat (Nyctophilus gouldi)

Cities are heterogeneous landscapes, with remnant vegetation interspersed amongst areas designed for human use. Native wildlife remaining in urban areas are only likely to thrive and persist if they incorporate human altered areas into what they perceive as habitat. Many sensitive species may be lost if they are restricted to remnant vegetation, and cannot use the urban matrix. In this study, we quantify spatial aspects of the ranging behaviour of Gould's long‐eared bat (Nyctophilus gouldi) using radio‐telemetry and acoustic surveys to determine use of the suburban–bushland interface. This species represents a group prone to extinction due to biological attributes that adapt it to flight within cluttered vegetation, making it more specialized. We radio‐tracked 19 individuals in Cumberland State Forest (CSF), a 40‐ha remnant located in north‐west Sydney, New South Wales, Australia. The nightly range (95% Kernel Density Estimator) was small and localized, and was no greater than 80 ha, where individuals moved on average less than 300 m from roosts each night. All individual N. gouldi tracked used bushland in an almost obligate manner, where up to 100% of used habitat was within local bushland, with little to no use of areas classified as ‘urban’ (residential, commercial and educational land uses). Small open spaces exposed to artificial lighting within the main ranging area of CSF had significantly lower activity (bat passes) of Nyctophilus spp. and significantly higher activity of other species more tolerant of urbanization (P < 0.05). Our results demonstrate that artificial lighting can ‘spill‐over’ into bushland and alter the use of preferred habitat. We conclude that large patches (>40 ha) of protected remnant vegetation must be managed to reduce further degradation, and smaller isolated patches could be restored to provide habitat, particularly in narrow bushland corridors, to assist these species to tolerate urban areas.     

Computer-assisted breast cancer grading

Morphological tumour differentiation has been shown in numerous studies to give a good prognosis in breast cancer, but as histological grading is based upon a subjective assessment of microscopical appearances, difficulities in consistency and reproducibility are inevitable. A review of the many conventional methods served to highlight a common limitation in their approach; lack of structure. We introduce a new approuch which seeks to overcome the problem, by formalizing the methods and identifying aspects which are well suited to computer aided analysis, these being incorporated into a microcomputer system facilitating the collection and appraisal of morphometric data. Within the Information Technology Institute (ITRI) at Brighton Polytechnic a research team is carrying out multidisciplinary work into the elucidation of biological systems. This programme, entitled ‘Intelligent Medical Systems’, used methods of mathematical signal processing and artificial intelligence, applied to a number of areas, one of which is decribed in this paper. The aim has been to utilize the inherent skill exercised by the histopathologist in interpreting microscopical images, whilst making quantilization more accurate and reproducible. the system has been developed within a highly structured framework and will have applications in teaching and routine histological analysis. The value of artificial intelligence techniques in the wider issues of this area is discussed.     

On models and muddles of heritability

One reason for the astonishing persistence of the IQ myth in the face of overwhelming prior and posterior odds against it may be the unbroken chain of excessive heritability claims for ‘intelligence’, which IQ tests are supposed to ‘measure’. However, if, as some critics insist, ‘intelligence’ is undefined, and Spearman's g is beset with numerous problems, not the least of which is universal rejection of Spearman's model by the data, then how can the heritability of ‘intelligence’ exceed that of milk production of cows and egg production of hens? The thesis of the present review paper is that the answer to this riddle has two parts: (a) the technical basis of heritability claims for human behavior is just as shaky as that of Spearman's g. For example, a once widely used ‘heritability estimate’ turns out to be mathematically invalid, while another such estimate, though mathematically valid, never fits any data; and (b) valid technical criticisms of flawed heritability claims typically are met with stubborn editorial resistance in the main stream journals, which tends to calcify such misinformation.     

Inhibition of 2A-mediated ‘cleavage’ of certain artificial polyproteins bearing N-terminal signal sequences

Where 2A oligopeptide sequences occur within ORFs, the formation of the glycyl–prolyl peptide bond at the C-terminus of (each) 2A does not occur. This property can be used to concatenate sequences encoding several proteins into a single ORF: each component of such an artificial polyprotein is generated as a discrete translation product. 2A and ‘2A-like’ sequences have become widely utilised in biotechnology and biomedicine. Individual proteins may also be co- and post-translationally targeted to a variety of sub-cellular sites. In the case of polyproteins bearing N-terminal signal sequences we observed, however, that the protein downstream of 2A (no signal) was translocated into the endoplasmic reticulum (ER). We interpreted these data as a form of ‘slipstream’ translocation: downstream proteins, without signals, were translocated through a translocon pore already formed by the signal sequence at the N-terminus of the polyprotein. Here we show this effect is, in fact, due to inhibition of the 2A reaction (formation of fusion protein) by the C-terminal region (immediately upstream of 2A) of some proteins when translocated into the ER. Solutions to this problem include the use of longer 2As (with a favourable upstream context) or modifying the order of proteins comprising polyproteins.     

Endophyte research: going beyond isolation and metabolite documentation

Many fungi belonging to mostly Ascomycota inhabit living tissues of plants of all major lineages without causing any visible symptoms. Termed horizontally transmitted endophytes, they have been investigated mostly for their capacity to produce bioactive secondary metabolites. However, many questions regarding the interactions between endophytes and their plant hosts, phytophagous insects and other fungi remain unanswered. This review highlights some of these areas of endophyte biology about which very little or no knowledge exists. Information garnered' using modern methodologies' on these grey areas of ‘endophytism’ (endophytic mode of lifestyle) would help immensely in understanding the evolution of endophytes of aerial plant tissues and in exploiting endophytes in various fields of biotechnology.     

Lignocellulose conversion and the future of fermentation biotechnology

The cost of many important fermentation products depends very strongly on the cost of the carbohydrate raw material. Even ‘high value’ products are not immune from these effects. The future scope and importance of the fermentation biotechnology industry will therefore depend in large measure on the cost of its carbohydrate raw materials. Lignocellulose conversion offers the potential for less expensive fermentable sugars. Two crucial research and development objectives to realize this potential are: (1) integrated use of all of the components of the heterogeneous lignocellulosic material (the ‘biomass refinery’ approach) and (2) the development of effective and economical pretreatments to increase the yield of glucose from cellulose hydrolysis.     

Number of genes controlling slow rusting resistance to leaf rust in five spring wheat cultivars

The number of genes controlling slow rusting resistance to leaf rust (Puccinia triticina) was estimated in five spring wheat (Triticum aestivum) cultivars using quantitative formulae. Parents and F₆ families were evaluated in replicated field trials under epidemics initiated by artificial inoculation. The F₆ families resulted from a diallel cross involving the fast-rusting cultivar Yecora 70 and five slow-rusting wheat cultivars: Sonoita 81, Tanager ‘S’, Galvez 87, Ures 81, and Moncho ‘S’. The area under the disease progress curve (AUDPC) was used to measure leaf rust severity over time. Results indicate that cultivar Sonoita 81 has three or four genes, Tanager ‘S’ has two or three genes, Galvez 87 has three genes, and both Ures 81 and Moncho ‘S’ have two genes for slow rusting resistance to leaf rust. Based on this result and previously reported moderate to high narrow-sense heritability estimates for slow rusting resistance in these materials, early-generation selection for slow leaf rusting would be effective.     

Mixotrophic in vitro cultivations: the way to go astray in plant physiology

Rate of photosynthesis and related plant carbohydrate status are crucial factors affecting plant vigor. Sugars providing carbon and energy sources serve also as important signaling molecules governing plant growth and development through a complex regulatory network. These facts are often neglected when mixotrophic cultivation of plants in vitro is used, where artificial exogenous sugar supply hinders studies of metabolism as well as sugar‐driven developmental processes. We compared the growth, selected gas‐exchange parameters and sugar metabolism characteristics in four model plants, potato (Solanum tuberosum ‘Lada’), tobacco (Nicotiana tabacum ‘Samsun’), rapeseed (Brassica napus ‘Asgard’) and strawberry (Fragaria vesca), under both photomixotrophic (PM) and photoautotrophic (PA) conditions. To ensure PA conditions, we used our improved sun caps that serve as gas and light permeable covers for cultivation vessels. We found bigger biomass accumulation, larger leaf areas, higher stomatal conductance and higher instantaneous water use efficiency and lower root sugar contents in PA plants compared to PM ones. However, for other characteristics (root biomass, root/shoot ratio, pigment contents, leaf sugar and starch levels and transpiration rates), a strong species‐dependent reactions to the exogenous sugar supply was noted, which does not allow to create a general view on the overall impact of PM nutrition under in vitro conditions.     

Invasive house geckos are more willing to use artificial lights than are native geckos

There is increasing concern about the ecological effects of light pollution, as artificial lighting spreads with urban expansion. While artificial lighting can negatively affect some species, others use it in novel ways. In tropical and subtropical regions, artificial lighting has created a novel niche: the ‘night light’ niche. Geckos living as human commensals (house geckos) are apparently well adapted to occupy this niche. In an urban area in north‐eastern Australia, we found that the invasive Asian house gecko Hemidactylus frenatus (Gekkonidae) occupies a broader range of light environments in the field than does the native gecko Gehyra dubia (Gekkonidae). Experimental removal of the invasive species from a building indicated that it did not behaviourally influence the light environments chosen by the native species in the short term; they continued to use darker areas even after the invasive species was removed. In Y‐maze experiments, neither species showed a significant preference for light or dark areas; however, preliminary data suggest the invasive species was more willing to explore the Y‐maze than the native species. The willingness of H. frenatus to forage closer to lights, where insect abundance is typically higher, might account for its success as a global invader of human environments, even in areas where other gecko species are established.     

Synthetic biology in society: learning from past experience?

Drawing an analogy to past debates over biotechnology, some stakeholders fear that synthetic biology (SB) could raise public concerns. Accordingly, ‘lessons from the past’ should be applied to avoid controversies. However, biotechnology in the 1990s is not the only possible comparator. The potential to become contested has been attributed to a number of other novel technologies. Looking at nanotechnology for example, controversies have not materialised to the extent predicted. The article discusses factors relevant for controversies over technologies as well as differences to the situation when modern biotechnology began to proliferate. Certain properties attributed to SB in the discussion so far indeed suggest a potential for controversies of its own, but perceptions may follow those on other aspects of biotechnology subject to local contingencies. Finally, it is questioned whether ELSI research should see its task in applying lessons from the past to ease technology introduction. Today, rather than seeing themselves being embedded in a linear model of technology development, social scientists take an interest in developments ‘upstream’ where technologies take shape.     

Improving the ‘tool box’ for robust industrial enzymes

The speed of sequencing of microbial genomes and metagenomes is providing an ever increasing resource for the identification of new robust biocatalysts with industrial applications for many different aspects of industrial biotechnology. Using ‘natures catalysts’ provides a sustainable approach to chemical synthesis of fine chemicals, general chemicals such as surfactants and new consumer-based materials such as biodegradable plastics. This provides a sustainable and ‘green chemistry’ route to chemical synthesis which generates no toxic waste and is environmentally friendly. In addition, enzymes can play important roles in other applications such as carbon dioxide capture, breakdown of food and other waste streams to provide a route to the concept of a ‘circular economy’ where nothing is wasted. The use of improved bioinformatic approaches and the development of new rapid enzyme activity screening methodology can provide an endless resource for new robust industrial biocatalysts.This mini-review will discuss several recent case studies where industrial enzymes of ‘high priority’ have been identified and characterised. It will highlight specific hydrolase enzymes and recent case studies which have been carried out within our group in Exeter.

     

From observational to actionable: rethinking omics in biologics production

As the era of omics continues to expand with increasing ubiquity and success in both academia and industry, omics-based experiments are becoming commonplace in industrial biotechnology, including efforts to develop novel solutions in bioprocess optimization and cell line development. Omic technologies provide particularly valuable ‘observational’ insights for discovery science, especially in academic research and industrial R&D; however, biomanufacturing requires a different paradigm to unlock ‘actionable’ insights from omics. Here, we argue the value of omic experiments in biotechnology can be maximized with deliberate selection of omic approaches and forethought about analysis techniques. We describe important considerations when designing and implementing omic-based experiments and discuss how systems biology analysis strategies can enhance efforts to obtain actionable insights in mammalian-based biologics production.     

Strategy for Stabilizing Enzymes Part Two: Increasing Enzyme Stability by Selective Chemical Modification

The molecular mechanisms of change in the thermal stability of proteins modified with low molecular weight reagents are discussed. The choice of stabilization mechanisms to be used as a general strategy for increasing enzyme stability by chemical modification is addressed. Hydrophilization of nonpolar surface areas is the most simple and reliable approach to artificial stabilization of enzymes for use in applied biochemistry and biotechnology.     

The relative contributions of refugium types to the persistence of benthic invertebrates in a seasonal snowmelt flood

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Expanding the applicability of cytochrome P450s and other haemoproteins

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