bluuebunny/crossref_metadata_2025 huggingface dataset:
Fossil fern rhizomes as a model system for biotic interactions across geologic time: Evidence from Patagonia
Authors: Bippus Alexander C. , Escapa Ignacio H. , Wilf Peter , Tomescu Alexandru M. F.
Published: January 2018

Background. A wealth of data on the networks of ecological interactions present in the modern biota can be readily obtained, due to the ease of unlimited access to the living organisms that form these networks. In contrast, understanding of such interactions in ecosystems of the geologic past is incomplete. Specifically, in terrestrial ecosystems we know comparatively little about plant biotic interactions besides herbivory, oviposition, galling. Here we describe a tiny in situ fossil community which sheds light on concurrent plant-plant, plant-fungal, and plant-animal interactions.

Methods. A single silicified osmundaceous rhizome from a new locality of the early Eocene (ca. 52 Ma) Tufolitas Laguna del Hunco was studied in serial thin sections using light microscopy. The community of organisms colonizing the tissues of the rhizome was characterized by identifying the organisms, as well as mapping and quantifying their distribution. For this, a 200 x 200 µm grid was superimposed onto the rhizome cross section and the colonizers present at each node of the grid were tallied.

Results. Preserved in situ, this community offers a rare window onto aspects of ancient ecosystems usually lost to time and taphonomic processes. The community is surprisingly diverse and includes the first fossilized leafy liverworts in South America, also marking the only fossil record of leafy bryophyte epiphytes; several types of fungal hyphae and spores; microsclerotia with probable affinities in several ascomycete families; and oribatid mite coprolites.

Discussion. The community associated with the Patagonian rhizome enriches our understanding of plant biotic interactions in the distant past and adds to a growing body of literature, which indicates that osmundaceous rhizomes were important hosts for component communities in ancient ecosystems, just as they are today. Because osmundaceous rhizomes represent an ecological niche that has remained unchanged over time and space, and are abundant in the fossil record, they provide a good paleoecological model system that could be used for exploring plant biotic interactions across geologic time.
Visitors’ emotional expression in urban forest parks: What can we know about on-line facial images from the Social Networking Services?
Authors: Guan Haoming , Wei Honxu , He Xingyuan , Ren Zhibin , Chen Xin , Guo Peng
Published: January 2018

Urban forests can attract visitors by the function of well-being improvement, which can be evaluated by analyzing the big-data from the social networking services (SNS). In this study, 935 facial images of visitors to nine urban forest parks were screened and downloaded from check-in records in the SNS platform of Sina Micro-Blog at cities of Changchun, Harbin, and Shenyang in Northeast China. Images were recognized for facial expressions by FaceReaderTM to read out eight emotional expressions: neutral, happy, sad, angry, surprised, scared, disgusted, and contempt. The number of images by women was larger than that by men. Compared to images from Changchun, those from Shenyang harbored higher neutral degree, which showed a positive relationship with the distance of forest park from downtown. In Changchun, the angry, surprised, and disgusted degrees decreased with the increase of distance of forest park from downtown, while the happy and disgusted degrees showed the same trend in Shenyang. In forest parks at city center and remote-rural areas, the neutral degree was positively correlated with the angry, surprised and contempt degrees but negatively correlated with the happy and disgusted degrees. In the sub-urban area the correlation of neutral with both surprised and disgusted degrees disappeared. Our study can be referred to by urban planning to evaluate the perceived well-being in urban forests through analyzing facial expressions of images from SNS.
Herbarium specimens can reveal impacts of climate change on plant phenology; a systematic review of methods and applications
Authors: Jones Casey A , Daehler Curtis C
Published: January 2018

Studies in plant phenology have provided some of the best evidence for large-scale responses to recent climate change. Over the last decade, more than thirty studies have used herbarium specimens to analyze changes in flowering phenology over time. In this review, we summarize the approaches and applications used to date. Reproductive plant phenology has primarily been analyzed using two summary statistics, the mean flowering day of year and first flowering day of year, but mean flowering day has proven to be a more robust statistic. Three types of regression models have been applied to test for changes in phenology; flowering day regressed on year, flowering day regressed on temperature, and temperature regressed on year. Most studies analyzed the effect of temperature by averaging temperatures from three months prior to the date of flowering, but other approaches may be suitable in some cases. On average, published studies have used 55 herbarium specimens per species to characterize changes in phenology over time, but in many cases fewer specimens were used. Geospatial grid data is increasingly being used for determining average temperatures at herbarium specimen collection locations, allowing testing for finer scale correspondence between phenology and climate. Multiple studies have shown that inferences from herbarium specimen data are comparable to findings from systematically collected field observations. Herbarium specimens are expected to become an increasingly important resource for analyzing plant responses to climate change. As temperatures continue to rise globally, there is a need to understand phenological rates of change in response to warming and implications of these changes, especially in tropical environments where phenological studies are thus far generally lacking.
Suitable oasis scales under a government plan in the Kaidu-Konqi River Basin of northwest arid region, China
Authors: Fu Aihong , Li Weihong , Chen Yaning , Liu Yuting
Published: January 2018

The Kaidu-Konqi River Basin was chosen as the study site in this paper in order to investigate suitable scales of natural and artificial oases with a specified water resource and water quantity planned by the local government. Combined with remote-sensing images in 2013, water resources in 2013, 2020 and 2030, and weather and socioeconomic data, suitable scales of oases were analyzed. The results showed that: (1) The total available water quantities in the Yanqi Basin and the Konqi River Basin without river base flow, and the input of water into Bosten Lake and Tarim River, over high-, normal and low-flow periods, in 2020 and 2030, were 19.04×108m3, 10.52×108m3, 4.95×108m3, 9.95×108m3 and 9.95×108m3, as well as 21.77×108m3, 13.95×108m3, 10.11×108m3, 12.50×108m3, and 9.74×108m3. (2) The water demand of the natural oasis in the Yanqi Basin and the Konqi River Basin was 5.33×108m3, and 5.91×108m3, respectively. (3) The total water consumption of the artificial oasis in 2013, 2020, and 2030 were 18.16×108m3, 17.63×108m3 and 17.63×108m3 in the Yanqi Basin, respectively, and 17.11×108m3, 16.54×108m3 and 16.54×108m3 in the Konqi River Basin, respectively. (4) Under government planning, the optimal area in 2020 and 2030 should be 3198.98 km2 in the Yanqi Basin oases, and 3858.87 km2 and 3081.17 km2 in the Konqi River Basin oases, respectively, under the different inflow variations, and 3129.07 km2 in the Yanqi Basin oases, and 3834.58 km2 and 3061.78 km2 in the konqi River Basin oases, respectively, under the appropriate proportion. (5) The natural and artificial oases in these basins should be greatly decreased in the future due to limited water resources.
Repeatability of glucocorticoid hormones in vertebrates: A meta-analysis
Authors: Schoenemann Kelsey L , Bonier Frances
Published: January 2018

We often expect that investigations of the patterns, causes, and consequences of among-individual variation in a trait of interest will reveal how selective pressures or ecological conditions influence that trait. However, many endocrine traits, such as concentrations of glucocorticoid (GC) hormones, exhibit adaptive plasticity and, therefore, do not necessarily respond to these pressures as predicted by among-individual phenotypic correlations. To improve our interpretations of among-individual variation in GC concentrations, we need more information about the repeatability of these traits within individuals. Many studies have already estimated the repeatability of baseline, stress-induced, and integrated GC measures, which provides an opportunity to use meta-analytic techniques to investigate 1) whether GC titers are generally repeatable across taxa, and 2) which biological or methodological factors may impact these estimates. From an intensive search of the literature, we collected 91 GC repeatability estimates from 47 studies. Overall, we found evidence that GC levels are repeatable, with mean repeatability estimates across studies ranging from 0.230 for baseline levels to 0.386 for stress-induced levels. We also noted several factors that predicted the magnitude of these estimates, including taxon, sampling season, and lab technique. Amphibians had significantly higher repeatability in baseline and stress-induced GCs than birds, mammals, reptiles, or bony fish. The repeatability of stress-induced GCs was higher when measured within, rather than across, life history stages. Finally, estimates of repeatability in stress-induced and integrated GC measures tended to be lower when GC concentrations were quantified using commercial kit assays rather than in-house assays. The extent to which among-individual variation in GCs may explain variation in organismal performance or fitness (and thereby inform our understanding of the ecological and evolutionary processes driving that variation) depends on whether measures of GC titers accurately reflect how individuals differ overall. Our findings suggest that while GC titers can reflect some degree of consistent differences among individuals, they frequently may not. We discuss how our findings contribute to interpretations of variation in GCs, and suggest routes for the design and analysis of future research.
The effect of tides on nearshore environmental DNA
Authors: Kelly Ryan , Gallego Ramón , Jacobs-Palmer Emily
Published: January 2018

Organisms of all kinds leave genetic traces in their environments, and in recent years, sequencing this environmental DNA (eDNA) has become a tractable means of surveying many species using water, air, or soil samples. The technique is beginning to become a core tool for ecologists, environmental scientists, and biologists of many kinds, but the temporal resolution of eDNA sampling is often unclear, limiting the ecological interpretations of the resulting datasets. Here, in a temporally and spatially replicated field study using ca. 330bp of eukaryotic COI mtDNA as a marker, we find that nearshore organismal communities are largely consistent across tides. Our findings suggest that nearshore eDNA tends to be endogenous to the site and water mass sampled, rather changing systematically as waters change over during the tidal cycle. However, where water-mass characteristics change, we find that the eDNA communities change in concert, again suggesting a close association between the habitat sampled and the eDNA community recovered.
Kill two birds with one stone: making multi-transgenic pre-diabetes mouse models through insulin resistance and pancreatic apoptosis pathogenesis
Authors: Kong Siyuan , Ruan Jinxue , Zhang Kaiyi , Hu Bingjun , Cheng Yuzhu , Zhang Yubo , Yang Shulin , Li Kui
Published: January 2018

Background. Type 2 diabetes, a chronic disease to which susceptibility is hereditary, is characterized by insulin resistance accompanied by defective insulin secretion. Mouse models, especially transgenic mice, play an important role in medical research. However, the transgenic mouse models that have been used in diabetes research are involved with single transgenes, focusing on the insulin gene or its mutants. Thus they mainly provide information related to Type 1 diabetes.

Methods. Here, we attempted to focus comprehensively on genes related to pancreatic islet damage, peripheral insulin resistance and related environmental inducing factors by generating single-transgenic mice (CHOP), dual-transgenic mice (hIAPP-CHOP) and triple-transgenic mice (11β-HSD1-hIAPP-CHOP). The latter two types of transgenic animals were induced with high-fat, high-sucrose diets (HFHSD). We evaluated and analyzed the diabetes-related symptoms and the histopathological and immunohistochemical features of the transgenic animals.

Results. Specifically, in the triple-transgene animals, the results of intraperitoneal glucose tolerance tests (IPGTT) began to change 60 days after induction (p<0.001). After 190 days of induction, the body weights (p<0.01) and plasma glucose levels of the animals in the Tg group were higher than those of the animals in the Nc group. After the mice were sacrificed, large amounts of lipid were found deposited in the adipose tissues (p<0.01) and ectopically deposited in the non-adipose tissues (p<0.05 or 0.01) of the animals in the Tg HFHSD group. The weights of the kidneys and hearts of the Tg animals were significantly increased (p<0.01). Serum C-P was decreased due to transgene effects, and insulin levels were increased due to the effects of the high-fat high-sucrose diet in the Tg HFHSD group, indicating that damaged insulin secretion and insulin resistance hyperinsulinemia existed simultaneously in these animals. The serum corticosterone levels of the animals in the Tg group were slightly higher than those of the Nc animals due to the effects of the 11βHSD-1 transgene and obesity. In the Tg HFHSD group, hepatic adipose deposition was more severe and the pancreatic islet area was enlarged under compensation, accompanying apoptosis. In the Tg ControlD group, hepatic adipose deposition was also severe, pancreatic islets were damaged, and their areas were decreased (p<0.05), and apoptosis of pancreatic cells occurred. Taken together, these data show that the transgenes led to early-stage pathological changes characteristic of type 2 diabetes in the triple-transgene HFHSD group. The disease of triple-transgenic mice was more severe than that of dual or single-transgenic mice.

Conclusion. The use of multi-transgenes involved in insulin resistance and pancreatic apoptosis is a better way to generate polygene-related early-stage diabetes models.
The hyolaryngeal apparatus of three species of Scinax (Scinaxinae: Hylidae: Anura) and comparison with other Hylidae species
Authors: Arenas Rodríguez Angélica , Hoyos Julio Mario
Published: January 2018

The larynx is an important morphological structure for sound production in frogs. Recently, high levels of variation in calls and their relation to the morphology of frogs in the family Hylidae, in addition to molecular data, have resulted in significant changes in the taxonomy of this family. However, there are few studies that describe the structures and processes of the hyoid, cricoid or arytenoid in hylid frogs. We studied the hyolaryngeal anatomy of both males and females of three species of the hylid genus Scinax (S. ruber, S. wandae and S. kennedyi) using differential and enzymatic clearing and staining methods. We describe the laryngeal anatomy of these species and compare to those of other hylids. We found that S. ruber has the largest cartilage arytenoid of any species of the family Hylidae studied to date. We show the laryngeal differences between Scinax species and the interspecific variability in the shapes of the projections among the arytenoid in the males of those species. The taxonomic characters described here can play a key role in differentiating these species from other members of Scinax, contributing to the knowledge of the species examined, and helping to differentiate them from other species, and to contributing also the natural history and phylogenetic relationships within the genus.
Use of seaweed Ulva lactuca for water bioremediation and as feed additive for white shrimp Litopenaeus vannamei
Authors: Elizondo-González Regina , Quiroz-Guzmán Eduardo , Escobedo-Fregoso Cristina , Magallón-Servín Paola , Peña-Rodríguez Alberto
Published: January 2018

Two experimental feeding trials were conducted during 4 weeks to evaluate the use of Ulva lactuca in shrimp culture: 1) for wastewater bioremediation in a water integrated system with U. lactuca, and 2) using different inclusion levels of U. lactuca meal in shrimp feed. In feeding trial 1, shrimp reared under integrated system with U. lactuca (SWE) resulted in similar growth and feed utilization as shrimp reared with normal water exchange (CWE). Shrimp under no water exchange (NWE) resulted in significant lower growth and higher feed conversion rate (FCR) compared to the other treatments (p < 0.05). Nitrogen compounds and phosphate in water from SWE and CWE treatments did not present significant differences during the experimental trial (p > 0.05). In feeding trial 2, seaweed biomass produced by wastewater bioremediation in SWE treatment were dried and ground to formulate diets containing 0, 1, 2, and 3% U. lactuca meal (0UL, 1UL, 2UL, and 3UL). Shrimp fed the 3UL diet resulted in a significant (p < 0.05) improvement of shrimp growth and FCR, and enhanced whole body lipid and carotenoid content by 30 and 60%, respectively, compared to control diet. Seaweed U. lactuca is suggested as a desirable species for wastewater bioremediation in integrated aquaculture systems, and its meal as good feed additive for farmed shrimp.
Scaling up freshwater macrozoobenthos metabarcoding with new BF2+BR2 fusion primer sets in 96-well format
Authors: Elbrecht Vasco , Steinke Dirk
Published: January 2018

The viability of DNA metabarcoding for assessment of freshwater macrozoobenthos has been demonstrated over the past years. It matured to a stage where it can be applied to monitoring at a large scale, keeping pace with increased high throughput sequencing (HTS) capacity. However, workflows and sample tagging need to be optimized to accommodate for hundreds of samples within a single sequencing run. We here conceptualize a streamlined metabarcoding workflow, in which samples are processed in 96-well plates. Each sample is replicated starting with tissue extraction. Negative and positive controls are included to ensure data reliability. With our newly developed fusion primer sets for the BF2+BR2 primer pair up to three 96-well plates (288 samples) can be uniquely tagged for a single Illumina sequencing run. By including Illumina indices tagging can by extended to thousands of samples. We hope that our metabarcoding workflow will be used as practical guide for future large-scale biodiversity assessments involving freshwater invertebrates. However, we also want to acknowledge that this is just one approach, and that we hope this article will stimulate discussion and publication of alternatives and extensions.
Expression pattern of Wif 1 during development of anorectum in fetal rats with anorectal malformations
Authors: Tang Xiao Bing , Li Huan , Zhang Jin , Wang Wei Lin , Yuan Zheng Wei , Bai Yu Zuo
Published: January 2018

Purpose: This study was performed to investigate the expression pattern of Wnt inhibitory factor 1 (Wif1) during anorectal development in normal and anorectal malformation (ARM) embryos and the possible role of Wif1 in the pathogenesis of ARM. Methods: ARM was induced with ethylenethiourea on the 10th gestational day in rat embryos. Cesarean deliveries were performed to harvest the embryos. The expression pattern of Wif1 protein and mRNA was evaluated in normal rat embryos (n=288) and ARM rat embryos (n=306) from GD13 to GD16 using immunohistochemical staining, Western blot, and real time RT-PCR. Results: Immunohistochemical staining revealed that in normal embryos Wif1 was constantly expressed in the cloaca from GD13 to GD16. On GD13 and GD14, Wif1-immunopositive cells were extensively expressed in the cloaca. On GD15, the expression of Wif1 were mainly detected on the very thin anal membrane. In ARM embryos, the epithelium of the hindgut and urorectal septum demonstrated faint immunostaining for Wif1 from GD14 to GD16. Western blot and real time RT-PCR revealed that Wif1 protein and mRNA expression level was significantly decreased in the ARM groups compared with the normal group on GD14 and GD15 (p<0.05).Conclusions: This study demonstrated that the expression pattern of Wif1 was disrupted in ARM embryos during anorectal morphogenesis, which demonstrated that downregulation of Wif1 at the time of cloacal separation into the primitive rectum and urogenital septum might related to the development of ARM.
Bacteria as “ink” for writing the initials of names on agar
Authors: Ng Wenfa
Published: January 2018

Microbes, while living in close proximity in biofilms, may in other cases not be closely localized in the environment. In the latter case, their interactions and communications are dependent on myriad factors such as existence of direct connections (e.g., web of hyphae from fungi) or pools of water where they could migrate. Hence, disparate groups of microbes could subsist on nutrients in their local microhabitat while maintaining weak communication links and metabolic exchanges with groups farther afield. But, how do we probe such distance dependent communications links between groups of microbes of the same or different species in the laboratory? Using a purple pigment producing bacterium as “ink” for writing on agar, a surface patterning technique was demonstrated to be a simple and relatively low cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates, which may find use in understanding possible interactions between different microbial species.Although a coarse surface patterning technique compared to more refined robot assisted patterning methods, simple spread plate deposition of different microbial species, in defined patterns, on separate areas of the agar surface, constituted a useful way forward in allowing us to delve deeper into the realmof understanding microbial interactions such as those in spatially resolved synthetic microbial community. Taking into account bacterial motility patterns, pigment diffusivity, and contrast of pigment with agar background color, inscription of patterns of bacterial cells through spread plate technique is an affordablemethod for lending a lens to spatially defined microbial interactions for microbial brethren unable to undergo migration on the agar surface. A synopsis of the work can be found in the accompanying PDF file, while the original article, “Bacterial calligraphy: A Memento for Undergraduate Research Students”, isavailable in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174, as an open access article. URL: http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v13i2.414
Patterning bacteria on agar for understanding distance mediated cell to cell signaling and metabolic exchanges
Authors: Ng Wenfa
Published: January 2018

Microbes, while living in close proximity in biofilms, may in other cases not be closely localized in the environment. In the latter case, their interactions and communications are dependent on myriad factors such as existence of direct connections (e.g., web of hyphae from fungi) or pools of water where they could migrate. Hence, disparate groups of microbes could subsist on nutrients in their local microhabitat while maintaining weak communication links and metabolic exchanges with groups farther afield. But, how do we probe such distance dependent communications links between groups of microbes of the same or different species in the laboratory? Using a purple pigment producing bacterium for “writing” on agar, a surface patterning technique was demonstrated to be a simple and relatively low cost tool for testing the feasibility of research ideas; for example, depositing cells in both straight and curvilinear lines on planar substrates, which may find use in understanding possible interactions between different microbial species. Although a coarse surface patterning technique compared to more refined robot assisted patterning methods, simple spread plate deposition of different microbial species, in defined patterns, on separate areas of the agar surface, constituted a useful way forward in allowing us to delve deeper into understanding microbial interactions such as those in spatially resolved synthetic microbial community. Taking into account bacterial motility patterns, pigment diffusivity, and contrast of pigment with agar background color, deposition of patterns of bacterial cells through spread plate technique is an affordable method for lending a lens to spatially defined microbial interactions for microbial brethren unable to undergo migration on the agar surface. A synopsis of the work can be found in the accompanying PDF file, while the original article, “Bacterial calligraphy: A Memento for Undergraduate Research Students”, is available in the Journal of Microbiology and Biology Education, Vol. 13, No. 2, pp. 172-174, as an open access article. URL: http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v13i2.414
Using question-and-answer and open-ended story-telling for unlocking creative potential in undergraduate research students
Authors: Ng Wenfa
Published: January 2018

The final year research project, a standard feature of most four year undergraduate curricula, aims to expose undergraduates to research as well as encourage them to use multiple perspectives in thinking creatively and critically about problems. Nevertheless, as most courses in earlier parts of the curriculum focus on well-defined problems with clear answers, a dichotomy exists between the research project’s desired educational outcomes and the undergraduates’ educational preparation. This often manifests as students’ inability at handling the ambiguities of research - which, in turn, leads to lack of motivation or trepidation at their projects. Such unintended negative educational outcomes are not necessarily due to students’ lack of creativity – and may have more to do with the difficulty of sparking students’ imagination with the paucity of pedagogical techniques available. From demonstrating experimental techniques to discussing new observations, postgraduates are the primary daily point-of-contact for undergraduates in the research lab. But how can postgraduates encourage undergraduates to think critically and creatively? One possibility lies in using common lab observations and experiences for unlocking students’ creative potential. In this abstract-only preprint, I describe two simple pedagogical tools for helping initiate the creative and critical thinking process in students. Specifically, I observed that using the Socratic approach – that is, question-and-answer - for guiding students in answering their own questions rather than directly providing the answers to them helped ignite the deductive and inductive thinking processes critical to tackling any research problem, as well as improving the students’ self-confidence in arriving at the answers. More important, the tentative steps taken in independent thinking also helped debunk their misconception that there exists a single correct answer for every question in research. Another pedagogical tool was the creative use of seemingly mundane electron and optical micrographs for constructing narratives unrelated to their subject matter. For example, an electron micrograph of a collection of particles poly-dispersed in size and shape was entitled, “Pebbles on the river bed,” with a storyline describing children playing happily in a clear stream and, upon looking down, saw small gravel and pebbles on the stream bed. Besides bringing a light-hearted moment into serious research work, such stories also illustrated the utility of thinking about a problem from multiple perspectives; specifically, discovering new and creative interpretations of an image. Collectively, through simple pedagogical tools such as question-and-answer, and open-ended story-telling, postgraduates can guide undergraduate students in thinking critically and creatively via demonstrating the thinking process involved in exploring different perspectives during problem-solving.
Brief history of computational chemistry: Three distinct eras and the relative importance of theoretical insights and computing power in advancing the field
Authors: Ng Wenfa
Published: January 2018

The past influence the present and future; for example, in computational chemistry, simplifying assumptions and approximations important to problem solving in the pre-computing era remains relevant today in allowing simulation of larger systems with reasonable amount of computer time. By highlighting significant milestones in efforts (theoretical and simulation) aimed at understanding the nature of chemical bond, a short essay traces the development and evolution of electronic structure calculation methods over the years. Placing the various methods along a time line and observing the temporal relationships between them reveals the clustering of methods into three distinct eras, each defined by their relative reliance on theory, approximations, experiment data and computing power for problem solution. Specifically, building of theoretical models for explaining spectroscopic emission spectra laid the foundation of the field when theory lagged behind experiment. Promulgation of the Schrodinger equation shifted the focus of the field towards developing methods for solving it. However, difficulty in solving the equation during the pre-computing era spawned an entire subfield seeking to develop increasingly refined methods for obtaining approximate solutions. Specifically, semi-empirical methods rely on experiment data to supply parameter values inaccessible through direct calculations from first principles, while approximate methods use simplifications to obviate the need for calculating cross interacting terms. Availability of large amount of inexpensive computing power in recent years brought forth ab initio (first principles) simulation methods capable of calculating electronic structure properties of large systems (e.g., long chain biomolecules) with few or no simplifying assumptions and at increasingly finer scales. However, high power computational resources are not easily accessible outside of research institutes. Hence, in what is known as coarse-graining, contemporary focus has been on developing methods for simulating, in high resolution, only important aspects of the problem while leaving other areas of the problem definition (i.e., simulation model) to coarser techniques, which in total, facilitates probing realistic system sizes for answers in sync with reality. The delineated chronological thread also provides the backdrop for asking counterfactual (“what if”) questions examining, from a historical vantage point, the relative roles of computing power and theoretical intuition in the development of computational chemistry. Contrary to widespread notions that advances in computational chemistry are solely potentiated by increases in computing power, the essay argues that the relationship between theoretical imagination and computing power is more nuanced: specifically, the two exert their influence at different junctures in the field’s evolution.
Brief history of computation chemistry: Three distinct eras and the relative importance of theoretical insights and computing power in advancing the field
Authors: Ng Wenfa
Published: January 2018

The past influences the present and future; for example, in computation chemistry, simplifying assumptions and approximations important in the pre-computing era remains relevant today in allowing simulation of larger systems with reasonable amount of computer time. By highlighting significant milestones in efforts (theoretical and simulation) aimed at understanding the nature of a chemical bond, a short essay traces the development and evolution of electronic structure calculation methods over the years. Placing the various methods along a time line and observing the temporal relationships between them reveals the clustering of methods into three distinct eras, each defined by their relative reliance on theory, approximations, experiment data and computing power for problem solution. Specifically, theoretical models built for explaining spectroscopic emission spectra laid the foundation of the field when theory lagged behind experiment. Promulgation of the Schrodinger equation – which describes total system energy and properties from a quantum mechanical perspective - shifted the focus of the field towards developing methods for solving the equation. However, difficulty in solving the Schrodinger equation during the pre-computing era spawned an entire subfield seeking to develop increasingly refined methods for obtaining approximate solutions. Specifically, semi-empirical methods rely on experiment data to supply parameter values inaccessible through direct calculations from first principles, while approximate methods use simplifications to obviate the need for calculating cross interacting terms. Availability of large amount of inexpensive computing power in recent years brought forth ab initio (first principles) simulation methods capable of calculating electronic structure properties of large systems (e.g., long chain biomolecules) with few or no simplifying assumptions and at increasingly small scales. But, high power computation resources are not easily accessible outside of research institutes. Hence, in what is known as coarse-graining, contemporary research focuses on developing methods for simulating, in high resolution, only important aspects of the problem while leaving other areas of the problem definition (simulation model) to coarser techniques. Together, coarse-graining facilitates probing realistic system sizes for answers in sync with reality. The delineated chronological thread also provides the backdrop for asking counterfactual (“what if”) questions examining, from a historical vantage point, the relative roles of computing power and theoretical intuition in the evolution of computation chemistry. Contrary to widespread notions that advances in computation chemistry are solely potentiated by increases in computing power, the essay argues that the relationship between theoretical imagination and computing power is more nuanced: specifically, the two exert their influence at different junctures in the field’s evolution.
Identifying microbes from environmental water samples in a discovery-based learning module
Authors: Ng Wenfa
Published: January 2018

What is the microbe that we are dealing with? Whether it is cholera or anthrax, we want to know the disease-causing microorganism as quickly as possible since prompt identification of the causative organism would help control disease spread - and potentially save lives through provision of appropriate care and medication. But despite the advent of rapid microbial identification tools – particularly those based on mass spectrometry – most undergraduate curricula continue to focus on culture- and nucleic acid-based identification techniques since they are widely used for detecting and identifying microbes in clinical and environmental samples. Mass spectrometry-based methods, however, have increasingly complemented traditional approaches in clinical and research laboratories - but are rarely featured in undergraduate curricula. Motivated by the desire to address the curriculum gap, I developed an inquiry-based laboratory exercise for introducing students to the operating principles and methodology of mass spectrometry-based microbial identification. By requiring students to identify microbes in environmental water samples – a real-life problem with unknown answers – the exercise piqued the students’ interest in learning, while helping to stir their curiosity through an interesting field activity where they put on a scientist’s hat in solving a mystery. This synopsis article summarizes a piece of published educational research and expands on the discussion of concepts underlying matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based microbial identification. For example, the article discusses the relative advantages and disadvantages of the pattern recognition and proteome database search approaches for analyzing mass spectra data. Additionally, the effect of general and tailored sample preparation protocols on identification accuracy is also elaborated. Finally, the pedagogical utility of field- and inquiry-based educational tools is also discussed in greater detail from a post-publication perspective.
Identifying microbes from environment water samples in a discovery-based learning module
Authors: Ng Wenfa
Published: January 2018

What is the microbe we are dealing with? Irrespective of cholera or anthrax, we want to know the disease causing microorganism as quickly as possible since prompt identification of the etiology organism would help control disease spread, and save lives through provision of appropriate care and medicine. But despite the promulgation of rapid microbe identification tools (such as those based on mass spectrometry), most undergraduate curricula continue to focus on culture and nucleic acid-based identification techniques since they are widely used for detecting and identifying microbes in clinical and environment samples. Mass spectrometry-based methods, however, have increasingly complemented traditional approaches in clinical and research laboratories - but they rarely feature in undergraduate curricula. Motivated by the desire to bridge the curriculum gap, I developed an inquiry-based laboratory exercise for introducing students to the operating principles and methodology of mass spectrometry enabled microbe identification. By requiring students to identify microbes in environment water samples (a real life problem with unknown answers), the exercise piqued the students’ interest in learning, while helping stir their curiosity in science through an interesting field activity where they put on a scientist’s hat in solving a mystery. This synopsis article summarizes a piece of published education research and expands on the discussion of concepts underlying matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) microbe identification. Specifically, the article discusses the relative advantages and disadvantages of the pattern recognition and proteome database search approaches for analyzing mass spectra data. In addition, the effect of different sample preparation protocols on identification accuracy is also discussed in detail. Finally, the pedagogy utility of field and inquiry-based education tools is also discussed in greater detail from a post-publication perspective. A full length synopsis of the work and a structured abstract can be found in the accompanying PDF file, while the original article, “Teaching Microbial Identification with Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) and Bioinformatics Tools”, and supplementary material is published in the Journal of Microbiology and Biology Education, Vol. 14, No. 1, pp. 103-106, and is available as an open access article at http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v14i1.494
Decussation as an axial twist: A Comment on Kinsbourne (2013)
Authors: de Lussanet Marc HE , Osse Jan W.M.
Published: January 2018

One of the great mysteries of the brain, which has puzzled all-time students of brain form and function, are the contralateral organization of the forebrain and the crossings of its major afferent and efferent connections. As a novel explanation, two recent studies have proposed that most of the forebrain is rotated by 180 degrees. Unfortunately, the latter study presented the first one in a misleading manner. We here discuss the similarities and differences between the two hypotheses.
Decussation as an axial twist: A Comment on Kinsbourne (2013)
Authors: de Lussanet Marc HE , Osse Jan W.M.
Published: January 2018

One of the great mysteries of the brain, which has puzzled all-time students of brain form and function is the contralateral organization of the forebrain, and the crossings of its major afferent and efferent connections. As a novel explanation, two recent studies have proposed that the rostral part of the head, including the forebrain, is rotated by 180 degrees with respect to the rest of the body (de Lussanet and Osse, 2012, Animal Biology 62, 193–216; Kinsbourne, 2013, Neuropsychology 27, 511–515). Kinsbourne proposes one 180-degree turn while we consider the 180 degrees being the result of two 90-degree turns in opposite directions. We discuss the similarities and differences between the two hypotheses.
Towards extracellular secretion of poly-β-hydroxybutyric acid (PHB) biodegradable polymer
Authors: Ng Wenfa
Published: January 2018

Plastics’ bioaccumulation and biomagnification potential, poor biodegradablility, and emission of hazardous chemicals during incineration, pose challenging disposal problems. Biodegradable, bio-renewable and biocompatible bacterial lipid-based storage polymer, poly-β-hydroxybutyric acids (PHB), offers a good functional replacement for petroleum-derived plastics. Originally nature’s solution for helping bacteria moderate fluctuations in nutrient availability, progressive elucidation of PHB biosynthetic pathway guided efforts aimed at overproducing the polymer via genetic engineering, or optimizing fermentation conditions and growth medium composition. Although increasing PHB production titer improves efficiency and reduces cost, the high price and lack of competitiveness of PHB in the consumer market stems largely from intracellular accumulation of PHB - where extraction and purification is the most significant cost component of PHB production. Additionally, use of toxic solvents and surfactants during PHB extraction may also contaminate the product. Thus, compared with increasing production titer, eliminating the extraction step would go further in reducing PHB’s relative price (cost), and improves production sustainability; thereby, motivating the development of techniques for inducing bacterial secretion of PHB. Given society’s goal of mitigating climate change through reducing dependence on petroleum-derived chemicals, extracellular secretion of PHB would also help realize a bio-feedstock based chemical industry – where secreted PHB serves as precursors for synthesizing a range of platform chemicals. By tuning the size of PHB inclusion bodies and targeting them to appropriate cellular exporters through pathway engineering, recent research has described the creation of a recombinant Escherichia coli strain capable of secreting substantial fraction of size-delimited PHB granules. Possible routes for increasing the amount of extracellularly exported PHB include: engineering PHB granules suitable for extracellular export, exploring and creating alternative export pathways and transporters through rational genetic engineering and/or directed evolution, and creating “leaky” bacterial strains for facile PHB secretion. Overall, achieving progress on one or more of the above challenges would help advance PHB’s role in a bio-renewable chemical industry. Additional topics such as the utility of PHB as bacterial storage polymers; the genes and metabolic pathways mediating its synthesis; and fermentation and extraction methods enabling its production provide context for a holistic discussion on the evolutionary origins, contemporary rediscovery and production of this incredibly useful and versatile biopolymer.
Towards extracellular secretion of poly-β-hydroxybutyric acid (PHB) biodegradable polymer
Authors: Ng Wenfa
Published: January 2018

Challenging disposal problems surround plastics use: mainly due to its poor biodegrability and emissions of hazardous chemicals during incineration. Poly-β-hydroxybutyric acids (PHB), a lipid based storage polymer in bacteria, is biodegradable, biorenewable and biocompatible. Progressive elucidation of PHB biosynthesis routes provides the understanding necessary for its production through recombinant microorganisms. Originally nature’s solution for helping bacteria moderate fluctuations in nutrient availability, PHB biosynthetic pathway has multiple nodes at which contemporary genetic engineering efforts for overproducing the polymer is focused on. Alternative means for increasing cellular PHB concentration include optimizing fermentation conditions and growth medium composition. But, intracellular accumulation of PHB (principally as inclusion bodies) and difficulty of extraction is the main reason for its high cost and lack of competitiveness. Hence, improving cost efficiency of extraction and purification are key areas for increasing PHB’s market competitiveness vis-à-vis petroleum derived plastics. Additionally, use of toxic solvents and surfactants during PHB extraction also expands its environmental footprint while also contaminating it. Thus, compared with increasing production titer, eliminating the extraction step would go further in reducing PHB’s relative price (cost), and improves environmental sustainability. But, high hydrophobicity induces PHB to amalgate into inclusion bodies, which points to the possibility of engineering microbes able to export PHB. Multiple pathways exist for protein export, but there is none for lipids. Hence, a myriad of recognition proteins, carrier proteins and transporters, and crucially, their recognition motifs for energy mediated (i.e., hydrolysis of ATP or GTP) transport of PHB through the likely lipid based transport channel must be constituted for extracellular secretion of PHB. Such a goal would require rational engineering of recognition, carrier, transport and channel proteins or their derivation from existing ones through directed evolution. The above possibility set sights on the future, but what is in store at the moment or the foreseeable future? Creating “leaky” bacteria strains for facile “export” of PHB may be a feasible path forward. “Leakiness” can be realized by using current recombinant DNA technology for overexpressing PHB in cells: (i) without a cell envelope, (ii) one with a significantly weakened one, or alternatively, (iii) a cell envelope or peptidoglycan layer with a random/engineered pore structure. Casting glances further out into the future, research into extracellular PHB secretion would likely open up avenues into recombinant bacteria production and export of lipid biopolymer or macromolecular complexes.