bluuebunny/crossref_metadata_2025 huggingface dataset:
Developmental Changes in Visual Responses to Social Interactions
Authors: Walbrin Jon , Mihai Ioana , Landsiedel Julia , Koldewyn Kami
Published: October 2019

Recent evidence demonstrates that a region of the posterior superior temporal sulcus (pSTS) is selective to visually observed social interactions in adults. In contrast, we know comparatively little about neural responses to social interactions in children. Here, we used fMRI to ask whether the pSTS would be ‘tuned’ to social interactions in children at all, and if so, how selectivity might differ from adults. This was investigated not only in the pSTS, but also in socially-tuned regions in neighbouring temporal cortex: extrastriate body area (EBA), face-selective STS (STS-F), fusiform face area (FFA), and temporo-parietal junction (TPJ-M).

Both children and adults showed selectivity to social interaction within right pSTS, while only adults showed selectivity on the left. Adults also showed both more focal and greater selectivity than children (6–12 years) bilaterally. Exploratory sub-group analyses showed that younger children (6–8 years), but not older children (9-12), are less selective than adults on the right, while there was a developmental trend (adults > older > younger) in left pSTS. These results suggest that, over development, the neural response to social interactions is characterized by increasingly more selective, more focal and more bilateral pSTS responses, a process that likely continues into adolescence.

Highlights

Children show less interaction selectivity in the pSTS than adults

Adults show bilateral pSTS selectivity, while children are more right-lateralized

Exploratory findings suggest interaction selectivity in pSTS is more focally tuned in adults
Stretching DNA to twice the normal length with single-molecule hydrodynamic trapping
Authors: Jiang Yan , Feldman Theodore , Bakx Julia A.M. , Yang Darren , Wong Wesley P.
Published: October 2019

Single-molecule force spectroscopy has brought many new insights into nanoscale biology, from the functioning of molecular motors, to the mechanical response of soft materials within the cell. To expand the single-molecule toolbox, we have developed a surface-free force spectroscopy assay based on a high-speed hydrodynamic trap capable of applying extremely high tensions for long periods of time. High-speed single-molecule trapping is enabled by a rigid and gas-impermeable microfluidic chip, rapidly and inexpensively fabricated out of glass, double-sided tape and UV-curable adhesive. Our approach does not require difficult covalent attachment chemistries, and enables simultaneous force application and single-molecule fluorescence. Using this approach, we have induced a highly extended state with twice the contour length of B-DNA in regions of partially intercalated double-stranded (dsDNA) by applying forces up to 250 pN. This highly extended state resembles the hyperstretched state of dsDNA, which was initially discovered as a structure fully intercalated by dyes under high tension. It has been hypothesized that hyperstretched DNA could also be induced without the aid of intercalators if high-enough forces were applied, which matches our observation. Combining force application with single-molecule fluorescence imaging is critical for distinguishing hyperstretched DNA from single-stranded DNA that can result from peeling. High-speed hydrodynamic trapping is a powerful yet accessible force spectroscopy method that enables the mechanics of biomolecules to be probed in previously difficult to access regimes.
Dataset Decay: the problem of sequential analyses on open datasets
Authors: Thompson William Hedley , Wright Jessey , Bissett Patrick G , Poldrack Russell A
Published: October 2019

Open data has two principal uses: (i) to reproduce original findings and (ii) to allow researchers to ask new questions with existing data. The latter enables discoveries by allowing a more diverse set of viewpoints and hypotheses to approach the data, which is self-evidently advantageous for the progress of science. However, if many researchers reuse the same dataset, multiple statistical testing may increase false positives in the literature. Current practice suggests that the number of tests to be corrected is the number of simultaneous tests performed by a researcher. Here we demonstrate that sequential hypothesis testing on the same dataset by multiple researchers can inflate error rates. This finding is troubling because, as more researchers embrace an open dataset, the likelihood of false positives (i.e. type I errors) will increase. Thus, we should expect a dataset’s utility for discovering new true relations between variables to decay. We consider several sequential correction procedures. These solutions can reduce the number of false positives but, at the same time, can prompt undesired challenges to open data (e.g. incentivising restricted access).
DNA Double Strand Break Repair inE. coliPerturbs Cell Division and Chromosome Dynamics
Authors: White M.A. , Darmon E. , Lopez-Vernaza M.A. , Leach D.R.F.
Published: October 2019

To prevent the transmission of damaged genomic material between generations, cells require a system for accommodating DNA repair within their cell cycles. We have previously shown thatEscherichia colicells subject to a single, repairable site-specific DNA double-strand break (DSB) per DNA replication cycle reach a new average cell length, with a negligible effect on population growth rate. We show here that this new cell size distribution is caused by a DSB repair-dependent delay in completion of cell division. This delay occurs despite unperturbed cell size regulated initiation of both chromosomal DNA replication and cell division. Furthermore, despite DSB repair altering the profile of DNA replication across the genome, the time required to complete chromosomal duplication is invariant. The delay in completion of cell division is accompanied by a DSB repair-dependent delay in individualization of sister nucleoids. We suggest that DSB repair events create inter-sister connections that persist until those chromosomes are separated by a closing septum.

Author Summary

The bacteriumEscherichia colihas a remarkable cell cycle where overlapping rounds of DNA replication can occur in a single generation between cell birth and division. This implies a complex coordination network between growth, genome duplication and cell division to ensure that the right number of genomes are created and distributed to daughter cells at all growth rates. This network must be robust to a number of unpredictable challenges. One such challenge is broken DNA, something that inE. coliis estimated to occur in ~20% of cell division cycles. In this work we perturb theE. colicell cycle by elevating the frequency of repairable DNA double-strand breaks to determine which parameters of the cell cycle are conserved and which are changed. Our results demonstrate that this perturbation does not alter the average cell size at initiation of DNA replication or initiation of cell division. Furthermore, it does not alter the time taken to replicate the genome or the generation time. However, it does delay the segregation of the DNA to daughter cells and the completion of cell division explaining the increase in average cell size observed previously.
Larviposition site selection mediated by volatile semiochemicals of larval origin in Glossina palpalis gambiensis
Authors: Geoffrey Gimonneau , Ouedraogo Romaric , Ernest Salou , Jean-Baptiste Rayaisse , Buatois Bruno , Solano Philippe , Dormont Laurent , Roux Olivier , Bouyer Jérémy
Published: October 2019

Tsetse flies (Diptera: Glossinidae) are the cyclical vectors of trypanosomes, the causative agents of African animal trypanosomosis or nagana in animals and human African trypanosomosis or sleeping sickness in humans. Tsetse flies are K-strategist species with the deposition of a single larva at 10 days intervals in specific sites. As larviposition site selection will strongly impact reproductive success, it is obvious that the selection of larviposition sites is not random and is under strong selective processes, probably mediated by specific cues as suggested by the existence of an aggregation factor in the Morsitans and Fusca groups. This study aimed to highlight the existence of an aggregation effect in the Palpalis group and to test for its chemical nature. We studied the larviposition site selection of Glossina palpalis gambiensis according to the presence of conspecific and heterospecific larvae buried in substrates in different settings. Three sets of experiments were performed with either individual or grouped (n = 50) gravid females, and with physical access to substrate or not. In both individual and grouped larviposition experiments, females selected significantly more often trays conditioned by larvae (P<0.005), either conspecific or heterospecific even in the absence of physical contact with the substrate. These results highlight the first evidence for larviposition site selection mediated by volatile semiochemicals of larval origin in Glossina palpalis gambiensis. However, these compounds seem not to be species-specific and therefore offer new avenues for the behavioural manipulation of these vectors and for the development of new vector control tools targeting gravid females.

Author summary

Larviposition site selection in tsetse flies is govern by several biotic and abiotic factors that lead to an aggregation effect of larvae. Among those, larvae are suspected to produce chemicals that drive females to breeding site but little information is available. This study aimed to highlight the existence of an aggregation effect of larval origin in the Palpalis group and to test for its chemical nature. Through behavioural larviposition choice experiments, we showed that females of Glossina palpalis gambiensis deposit their larvae significantly more often in trays conditioned either by conspecific or heterospecific larvae, even in the absence of physical contact with the substrate. These results highlight the first evidence for aggregation effect in Glossina palpalis gambiensis mediated by volatile semiochemicals of larval origin. Isolation and identification of these chemicals should offer new avenues for the behavioural manipulation of these vectors and for the development of new vector control tools targeting gravid females.
Optogenetic mapping of feeding and self-stimulation within the lateral hypothalamus of the rat
Authors: Urstadt Kevin R. , Berridge Kent C.
Published: October 2019

The lateral hypothalamus (LH) regulates eating and motivation, and includes several anatomical subregions. This study explored localization of function across different LH subregions in controlling food intake stimulated by optogenetic channelrhodopsin excitation, and in supporting laser self-stimulation. We particularly compared the tuberal LH, the posterior LH, and the lateral preoptic area. Local diameters of tissue optogenetically stimulated within LH were assessed by measuring laser-induced Fos plumes and Jun plumes via immunofluorescence surrounding optic fiber tips, and were used to map localization of function for effects elicited by LH optogenetic stimulation. Optogenetic stimulation of the tuberal subsection of the LH behaviorally produced the most robust food intake initially, but produced only mild laser self-stimulation in the same rats. However, after repeated exposures to optogenetic stimulation, tuberal LH behavioral profiles shifted toward more self-stimulation and less food intake. By contrast, stimulation of the lateral preoptic area produced relatively little food intake or self-stimulation, either initially or after extended stimulation experience. Stimulation in the posterior LH subregion supported moderate self-stimulation, but not food intake here, and at higher laser intensity shifted valence to evoke escape behaviors. We conclude that the tuberal LH subregion may best mediate increases in food intake stimulated by optogenetic excitation. However, incentive motivational effects of tuberal LH stimulation may shift toward self-stimulation behavior after repeated stimulation. By contrast, the lateral preoptic area and posterior LH do not as readily elicit either eating behavior or laser self-stimulation, and may be more prone to higher-intensity aversive effects.
Truncated WT1 protein isoform expression is increased in MCF-7 cells in a long-term estrogen depletion
Authors: Santiago Saavedra-Alonso , Pablo Zapata-Benavides , Edgar Mendoza-Gamboa , Ana Karina Chavez-Escamilla , Mariela Arellano-Rodríguez , Cristina Rodriguez-Padilla
Published: October 2019

Background

The WT1 gene codes for a transcription factor that presents several protein isoforms with diverse biological properties, capable of positively and negatively regulating genes involved in proliferation, differentiation, and apoptosis. WT1 protein is overexpressed in more than 90% of breast cancer, however, its role during tumor progression is still unknown.

Methodology

In this work were analyzed the expression of WT1 isoforms (36-38 kDa and 52-54 kDa, and 17 AA (+/−) and KTS (+/−)) in breast cancer cells. On the other hand, with the purpose of mimicking the process of switch from a hormone-dependent to a hormone-independent neoplasm, an assay was performed using the MCF-7 cells cultured in long-term estrogen depletion (MCF-7 LTED cells) to determine the WT1 protein isoforms expression by western blot and RT-PCR, and Her2/neu and Estrogen receptor (ER) expression by quantitative RT-PCR assay. Growth kinetics and sensitivity to tamoxifen were performed in the MCF-7 LTED cells by trypan blue exclusion.

Results

The western blot shows the presence of the 52-54 kDa WT1 isoform in the ER (+) breast cancer cells, but not in the ER (−) cells. The 36-38 kDa WT1 isoform was detected in all the breast cancer cell lines analyzed. Using specific primers was found that 17 AA (+) / KTS (−) WT1 isoform was the most frequent in four breast cancer cell lines. During the sampling of the MCF-7 cells in estrogen depletion, an increase in the short-term of 52-54 kDa WT1 isoform was observed and this was kept until week 13, thereafter, its expression was absent; alternately, the 36-38 kDa WT1 isoform was observed from week 1 and it remained constant until week 27. MCF-7 LTED cells growth kinetic decreased 1.4 folds and were not sensitive to tamoxifen antiproliferative effect (p ≤ 0.05). Finally, were observed an increase of expression of ER and Her2/neu in the MCF-7 LTED cells.

Conclusions

The 36-38 kDa WT1 isoform expression occurs during the modifications of the hormonal environment, suggesting that it may be playing an important role in its adaptation and tumor progression.
Mechanochemical Model of Transcriptional Bursting
Authors: Klindziuk A. , Meadowcroft B. , Kolomeisky A. B.
Published: October 2019

Populations of genetically identical cells generally show a large variability in cell phenotypes, which is typically associated with the stochastic nature of gene expression processes. It is widely believed that a significant source of such randomness is the transcriptional bursting, which is when periods of active production of RNA molecules alternate with periods of RNA degradation. However, the molecular mechanisms of such strong fluctuations remain unclear. Recent studies suggest that DNA supercoiling, which happens during transcription, might be directly related to the bursting behavior. Stimulated by these observations, we developed a stochastic mechano-chemical model of supercoiling-induced transcriptional bursting where the RNA synthesis leads to the buildup of torsion in DNA. This slows down the RNA production until binding of an enzyme gyrase to DNA, which releases the stress and allows for the RNA synthesis to restart with the original rate. Using a thermodynamically consistent coupling between mechanical and chemical processes, dynamic properties of transcription are explicitly evaluated. In addition, a first-passage method to evaluate the dynamics of transcription is developed. Theoretical analysis shows that the transcriptional bursting is observed when both the supercoiling and the mechanical stress-release due to gyrase are present in the system. It is also found that the overall RNA production rate is not constant and depends on the number of previously synthesized RNA molecules. A comparison with experimental data on bacteria allows us to evaluate the energetic cost of supercoiling during transcription. It is argued that the relatively weak mechanochemical coupling allows transcription to be regulated most effectively.

SIGNIFICANCE

Transcriptional bursting has been cited as one of the probable causes of phenotypic differences in cells with identical genomes. However, the microscopic origin of noisy dynamics in RNA production remains unclear. We developed a thermodynamically-consistent mechano-chemical stochastic model, which, via explicit calculations of dynamic properties, provides a consistent physical-chemical description of how the supercoiling of DNA together with enzymatic activity of gyrases produce transcriptional bursting. It also allows us to explain that the coupling between mechanical and chemical processes might be the reason for efficient regulation of transcription.
The hare, tortoise and crocodile revisited: Tree fern facilitation of conifer persistence and angiosperm growth in simulated forests
Authors: Brock James M. R. , Morales Narkis S. , Burns Bruce R. , Perry George L. W.
Published: October 2019

Forests in which conifers and angiosperms coexist in the canopy with a well‐developed understorey/subcanopy have often been conceptualized as three component systems. In these systems, the coexistence and regeneration of the two canopy tree components may be mediated by a third component in the understory and/or subcanopy, for example, palms, bamboo or tree ferns. However, the effect of this understorey/subcanopy component has only been studied over short time periods relative to the longevities (centuries) of the canopy species.

Simulation models provide a way to evaluate the inter‐generational consequences of patterns and mechanisms observed over short temporal extents. We extended a spatially explicit individual‐based simulation model representing the dynamics of New Zealand mixed conifer–angiosperm forest by including a growth form representing tree ferns (the third component). Using model‐based experiments, we evaluated the effects of varying initial densities of tree ferns, the contributions of external propagule sources and the long‐term effects of macro‐litterfall and suppressed seedling density by tree ferns on forest composition and structure over 2,500 years.

The model accurately reproduced observed tree fern growth patterns (height and age distributions) in old‐growth forests, patterns of species replacement and dominance hierarchies in forest succession. The outcomes of the model experiments suggested that shade‐intolerant conifers persist longer and grow older and taller with increasing tree fern density. Although angiosperm stem density reduced along the same series, their longevities and heights also increased with tree fern density. We suggest that these increases are due to conifer and angiosperm trees experiencing reduced competition from neighbouring trees associated with tree ferns increasingly occupying spaces between trees. Over centuries of simulation, the population‐level effect of seedling suppression beneath tree ferns suggests an emergent pattern of negative density dependence in understorey tree ferns.

Synthesis. Tree fern understories are important determinants of forest structure, partially releasing shade‐intolerant conifers from angiosperm competition, reducing angiosperm density and, therefore, competition intensity in northern New Zealand forests. In many forest ecosystems, conifer–angiosperm forest dynamics can be conceptualized as three component systems.
Metabolic syndrome and semen quality in adult population
Authors: Chen Yuan‐Yuei , Kao Tung‐Wei , Peng Tao‐Chun , Yang Hui‐Fang , WU Chen‐Jung , Chen Wei‐Liang
Published: October 2019

Background

Male obesity is suggested to impact negatively on male fertility and semen quality in numerous studies. However, previous literatures regarding health effects of the metabolic syndrome (MetS) on semen quality are rare and inconsistent. The aim of this study is to investigate the relationship between MetS and sperm parameters in a Taiwanese reproductive‐age male population.

Methods

A total of 8395 men who attended a private medical screening program in Taiwan from 2010 to 2016 were included in this cross‐sectional study. Semen analysis was assessed in accordance with the WHO guidelines and included sperm concentration, total motility, progressive motility, and morphology. MetS was defined by the modified National Cholesterol Education Program Third Adult Treatment Panel (NCEP ATP III) criteria with the Asian cutoff for waist circumference (WC). The associations between MetS and semen analysis were examined by multivariable linear regressions.

Results

After fully adjusting for pertinent covariables, MetS was significantly associated with a reduced percentage of sperm normal morphology. Blood pressure, WC, and serum glucose had a significantly negative association with sperm normal morphology. Individuals with an increased number of MetS components had a closer association with reduced sperm progressive motility and the percentage of normal morphology.

Conclusion

MetS and its components exhibited deleterious effects on semen quality among reproductive‐age men. Further studies are warranted to explore these pathophysiologic relationship and underlying mechanisms.
The presence of Aspergillus fumigatus in asthmatic airways is not clearly related to clinical disease severity
Authors: Sullivan Ashley , Hunt Eoin B. , Ward Chris , Lapthorne Susan , Eustace Joseph A. , Fanning Liam J. , Plant Barry J. , O'Byrne Paul M. , MacSharry John A. , Murphy Desmond M.
Published: October 2019

Background

It is suggested that airway fungi, in particular Aspergillus may impinge on clinical phenotype in asthma. Indeed, the term severe asthma with fungal sensitization (SAFS) has been coined. We aimed to ascertain whether the presence of fungi, in particular Aspergillus fumigatus, in the airway correlated with asthma severity and control. Furthermore, we aimed to determine whether traditional markers of Aspergillus sensitization related to the presence of Aspergillus within the airway.

Methods

Sixty‐nine patients characterized by asthma severity (GINA) and level of control (ACQ‐7) underwent bronchoscopy and bronchoalveolar lavage (BAL). Serum was assessed for A fumigatus‐specific IgE and total IgE. Galactomannan and relevant cytokine levels were assessed in serum, plasma and BAL. BAL was analyzed for the presence of A fumigatus.

Results

In BAL, fungi were visible by microscopy in 70% and present by qPCR in 86% of patients, while A fumigatus was detectable by qPCR in 46%. Plasma and BAL IL‐4, IL‐6, IL‐10, IL‐13 and TNF‐α correlated with BAL fungal presence, while plasma IL‐17 correlated with BAL fungal presence. Aspergillus positive BAL correlated with increased plasma and BAL IL‐6 and BAL IL‐13. There was no relationship between fungal airway presence and steroid dose, asthma severity or control. The presence of Aspergillus within the airway did not relate to serum IgE positivity for Aspergillus.

Conclusions

Fungi were present in a large proportion of our asthmatic patients’ airways, but their presence was not predicted by traditional markers of sensitization, nor did it appear to be related to measures of disease severity or control.
PGC‐1α plays a pivotal role in simvastatin‐induced exercise impairment in mice
Authors: Panajatovic Miljenko Valentin , Singh François , Roos Noëmi Johanna , Duthaler Urs , Handschin Christoph , Krähenbühl Stephan , Bouitbir Jamal
Published: October 2019

Aim

Statins decrease cardiovascular complications, but can induce myopathy. Here, we explored the implication of PGC‐1α in statin‐associated myotoxicity.

Methods

We treated PGC‐1α knockout (KO), PGC‐1α overexpression (OE) and wild‐type (WT) mice orally with 5 mg simvastatin kg−1 day−1 for 3 weeks and assessed muscle function and metabolism.

Results

In WT and KO mice, but not in OE mice, simvastatin decreased grip strength, maximal running distance and vertical power assessed by ergometry. Post‐exercise plasma lactate concentrations were higher in WT and KO compared to OE mice. In glycolytic gastrocnemius, simvastatin decreased mitochondrial respiration, increased mitochondrial ROS production and free radical leak in WT and KO, but not in OE mice. Simvastatin increased mRNA expression of Sod1 and Sod2 in glycolytic and oxidative gastrocnemius of WT, but decreased it in KO mice. OE mice had a higher mitochondrial DNA content in both gastrocnemius than WT or KO mice and simvastatin exhibited a trend to decrease the citrate synthase activity in white and red gastrocnemius in all treatment groups. Simvastatin showed a trend to decrease the mitochondrial volume fraction in both muscle types of all treatment groups. Mitochondria were smaller in WT and KO compared to OE mice and simvastatin further reduced the mitochondrial size in WT and KO mice, but not in OE mice.

Conclusions

Simvastatin impairs skeletal muscle function, muscle oxidative metabolism and mitochondrial morphology preferentially in WT and KO mice, whereas OE mice appear to be protected, suggesting a role of PGC‐1α in preventing simvastatin‐associated myotoxicity.
Clinicopathologic and immunophenotypic characterization of lichen planopilaris and central centrifugal cicatricial alopecia: A comparative study of 51 cases
Authors: Jordan Christian S. , Chapman Cindi , Kolivras Athanassios , Roberts Janet L. , Thompson Nathaniel B. , Thompson Curtis T.
Published: October 2019

Background

The purpose of the study was to compare the histopathologic and immunophenotypic features of central centrifugal cicatricial alopecia (CCCA) and lichen planopilaris (LPP) to better characterize and differentiate these two clinical entities. CCCA remains an ill‐defined and still‐unsettled histologic entity and many hair loss experts regard CCCA to be histologically indistinguishable from LPP. Given the overlapping histologic features of these two lymphocyte‐predominant cicatricial alopecias, and the lack of consensus regarding the significance of proposed distinctions, dermatopathologists face difficulty in providing clinicians and patients certainty with a definitive diagnosis of CCCA vs LPP.

Methods

We performed a retrospective review of 51 scalp biopsies of patients with either the clinical diagnosis of CCCA (27 cases) or LPP (24 cases). Clinical information, histologic features of hematoxylin‐eosin‐stained sections, and a panel of immunohistochemical markers were evaluated on scalp biopsies. Tested parameters were quantified, and statistical analysis was performed.

Results

Our study found no differences on either histologic assessment or immunophenotypic characterization between cases of classic LPP and CCCA.

Conclusion

The conclusion of this study is that the inflammatory infiltrates in CCCA and LPP are not only histologically similar but also immunophenotypically indistinguishable.
A major facilitator superfamily transporter in Colletotrichum fructicola (CfMfs1) is required for sugar transport, appressorial turgor pressure, conidiation and pathogenicity
Authors: Chen Yanying , Zhou Guoying , Liu Junang
Published: October 2019

The major facilitator superfamily (MFS) is one of the largest membrane‐protein families. To investigate the role of MFS proteins in the fungal plant anthracnose pathogen Colletotrichum fructicola, the CfMFS1 gene was deleted. This resulted in reduced mycelial growth, conidial yield and decreased virulence on tea oil camellia leaves. In addition, ∆Cfmfs1 showed increased sensitivity to osmotic stress and to a cell‐wall stressor. Further analysis revealed that CfMfs1 is required for conidial penetration and appressorial turgor pressure, both important for fungal pathogen invasion. Confocal fluorescence microscopy showed that CfMfs1 is localized to membranes of both hyphae and conidia, suggesting that it may be a membrane transporter. Our study provides evidence that CfMfs1 has a role in conidiation, sugar transport, stress response, conidial penetration, appressorial turgor pressure and virulence against tea oil camellia.
Structure of the Cannabis sativa olivetol‐producing enzyme reveals cyclization plasticity in type III polyketide synthases
Authors: Kearsey Lewis J. , Prandi Nicole , Karuppiah Vijaykumar , Yan Cunyu , Leys David , Toogood Helen , Takano Eriko , Scrutton Nigel S.
Published: October 2019

In the native pathway to therapeutic cannabinoid biosynthesis in Cannabis sativa, the three‐step production of a key intermediate, olivetolic acid, is catalysed by the enzymes tetraketide synthase (TKS; linear tetraketide intermediate production in two stages) and olivetolic acid cyclase (OAC; final C2 → C7 aldol condensation). In the absence of OAC, a nonenzymatic C2 → C7 decarboxylative aldol condensation of the tetraketide intermediate occurs forming olivetol. TKS is a type III polyketide synthase, and the question arises why it is unable to form olivetolic acid directly, but instead forms this unwanted side product. We determined the TKS, CoA complex structure, and performed structurally guided mutagenesis studies to identify potential residues responsible for cyclization pathway discrimination in type III polyketide synthases. Prior studies suggested an ‘aldol switch’ is necessary to allow linear tetraketide intermediate release prior to cyclization, thereby enabling subsequent olivetolic acid production by OAC. However, our studies do not support the presence of a universal or predictable ‘aldol switch’ consensus sequence. Instead, we propose the mode of ordered active site water activation between type III polyketide synthases catalysing different cyclization mechanisms is subtle and homologue‐specific. Our work indicates that subtle structural variations between homologous enzymes can have a major mechanistic impact on the catalytic outcome. This highlights the importance of embedding high‐resolution structural analysis of multiple enzyme homologues with classical site‐directed mutagenesis studies when investigating highly similar enzymes with different mechanistic pathway outcomes.

Enzymes

TKS, EC 2.3.1.206; OAC, EC 4.4.1.26; chalcone synthase, EC 2.3.1.74; stilbene synthase, EC 2.3.1.95; 2‐PS, EC 2.3.1.-.

Accession numbers

The atomic coordinates and structure factors for the crystal structure of TKS have been deposited in the Protein Data Bank with accession number 6GW3.
Stabilization of backbone‐circularized protein is attained by synergistic gains in enthalpy of folded structure and entropy of unfolded structure
Authors: Shibuya Risa , Miyafusa Takamitsu , Honda Shinya
Published: October 2019

Backbone circularization is an effective technique for protein stabilization. Here, we investigated the effect of a connector, an engineered segment that connects two protein termini, on the conformational stability of previously designed circularized variants of granulocyte colony‐stimulating factor (G‐CSF). Heat tolerance and chemical denaturation analyses revealed that aggregation resistance and thermodynamic stability of the circularized variants were superior to those of linear G‐CSF. Crystal structure and molecular dynamics (MD) simulation of the most thermodynamically stable variant (C166) revealed a high number of intramolecular hydrogen bonds in both the connector region and Helix D adjacent to the connector region in the folded structure. MD simulations and theoretical calculations involving different force fields indicated a reduction in the main chain entropy of C166 in the unfolded state and increase in the intramolecular hydrogen bond energy of C166 in the folded structure. Although backbone circularization is usually considered to alter chain entropy of the unfolded state, the data indicated that it could also improve the conformational enthalpy of the folded state. Further structural examination of the connector region confirmed that protein design based on a statistical analysis of local structures is an effective approach for predicting an optimum connector length to improve the conformational stability of backbone‐circularized proteins. Protein design using backbone circularization with an optimum connector length will be useful for the development of effective and safe protein therapeutics.

Database

Structural data are available in Protein Data Bank under the accession number 5ZO6.
Mutations in the Scn8a DIIS4 voltage sensor reveal new distinctions among hypomorphic and null Nav1.6 sodium channels
Authors: Inglis George Andrew S. , Wong Jennifer C. , Butler Kameryn M. , Thelin Jacquelyn T. , Mistretta Olivia C. , Wu Xuewen , Lin Xi , English Arthur W. , Escayg Andrew
Published: October 2019

Mutations in the voltage‐gated sodium channel gene SCN8A cause a broad range of human diseases, including epilepsy, intellectual disability, and ataxia. Here we describe three mouse lines on the C57BL/6J background with novel, overlapping mutations in the Scn8a DIIS4 voltage sensor: an in‐frame 9 bp deletion (Δ9), an in‐frame 3 bp insertion (∇3) and a 35 bp deletion that results in a frameshift and the generation of a null allele (Δ35). Scn8a
Δ9/+ and Scn8a
∇3/+ heterozygous mutants display subtle motor deficits, reduced acoustic startle response, and are resistant to induced seizures, suggesting that these mutations reduce activity of the Scn8a channel protein, Nav1.6. Heterozygous Scn8a
Δ35/+ mutants show no alterations in motor function or acoustic startle response, but are resistant to induced seizures. Homozygous mutants from each line exhibit premature lethality and severe motor impairments, ranging from uncoordinated gait with tremor (Δ9 and ∇3) to loss of hindlimb control (Δ35). Scn8a
Δ9/Δ9 and Scn8a
∇3/∇3 homozygous mutants also exhibit impaired nerve conduction velocity, while normal nerve conduction was observed in Scn8a
Δ35/Δ35 homozygous mice. Our results suggest that hypomorphic mutations that reduce Nav1.6 activity will likely result in different clinical phenotypes compared to null alleles. These three mouse lines represent a valuable opportunity to examine the phenotypic impacts of hypomorphic and null Scn8a mutations without the confound of strain‐specific differences.
Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions
Authors: Rosenfeld Cheryl S. , Hekman Jessica P. , Johnson Jennifer L. , Lyu Zhen , Ortega Madison T. , Joshi Trupti , Mao Jiude , Vladimirova Anastasiya V. , Gulevich Rimma G. , Kharlamova Anastasiya V. , Acland Gregory M. , Hecht Erin E. , Wang Xu , Clark Andrew G. , Trut Lyudmila N. , Behura Susanta K. , Kukekova Anna V.
Published: October 2019

The underlying neurological events accompanying dog domestication remain elusive. To reconstruct the domestication process in an experimental setting, silver foxes (Vulpes vulpes) have been deliberately bred for tame vs aggressive behaviors for more than 50 generations at the Institute for Cytology and Genetics in Novosibirsk, Russia. The hypothalamus is an essential part of the hypothalamic‐pituitary‐adrenal axis and regulates the fight‐or‐flight response, and thus, we hypothesized that selective breeding for tameness/aggressiveness has shaped the hypothalamic transcriptomic profile. RNA‐seq analysis identified 70 differentially expressed genes (DEGs). Seven of these genes,DKKL1,FBLN7,NPL,PRIMPOL,PTGRN,SHCBP1LandSKIV2L, showed the same direction expression differences in the hypothalamus, basal forebrain and prefrontal cortex. The genes differentially expressed across the three tissues are involved in cell division, differentiation, adhesion and carbohydrate processing, suggesting an association of these processes with selective breeding. Additionally, 159 transcripts from the hypothalamus demonstrated differences in the abundance of alternative spliced forms between the tame and aggressive foxes. Weighted gene coexpression network analyses also suggested that gene modules in hypothalamus were significantly associated with tame vs aggressive behavior. Pathways associated with these modules include signal transduction, interleukin signaling, cytokine‐cytokine receptor interaction and peptide ligand‐binding receptors (eg, G‐protein coupled receptor [GPCR] ligand binding). Current studies show the selection for tameness vs aggressiveness in foxes is associated with unique hypothalamic gene profiles partly shared with other brain regions and highlight DEGs involved in biological processes such as development, differentiation and immunological responses. The role of these processes in fox and dog domestication remains to be determined.
Variation in Saturated Hydraulic Conductivity at the Outcrop Scale, the Whanganui Basin, New Zealand
Authors: Rees Callum , Palmer Alan , Palmer Julie , Singh Ranvir
Published: October 2019

Groundwater flow and contaminant transport are strongly influenced by hydrogeological spatial variation. Understanding the textural heterogeneity of aquifer and aquitard units is critical for predicting preferential flow pathways, but is often hindered by sparse hydrogeological data, widely spaced data points, and complex stratigraphy. Here, we demonstrate the application of a relatively new air permeameter technology, providing a cost‐effective, rapid alternative for characterizing hydrostratigraphic units in the field. The aim of this research is to (1) characterize the variation of saturated hydraulic conductivity across shallow‐marine hydrostratigraphic units of the Whanganui Basin, New Zealand, and (2) assess the variation of saturated hydraulic conductivity within individual hydrostratigraphic units and relate these changes to facies and depositional environments. Results suggest heterogeneity within fine‐grained aquitard units is controlled by bioturbation, whereby burrowing, ingestion and defecation results in grain size segregation and differential micrite cementation. Coarse‐grained heterolithic aquifer facies display sharp changes in permeability across planar to cross‐bedded sets, related to current and wave energy fluctuations within shallow‐marine depositional settings. Bedding plane orientation creates high permeability zones that promotes down dip subsurface flow. Down dip gradation of coarse‐grained nearshore facies into fine‐grained shelf facies along the paleo shoreline‐shelf transect is suggested to promote lateral and vertical groundwater flow within the basin fill. Air permeameter techniques have potential for application within groundwater basins around the world, providing datasets that facilitate greater understanding of groundwater systems, informing practices and policies for targeted water quality management.
Pain and Pruritus: a study of their similarities and differences
Authors: Anzelc Madison , Burkhart Craig G.
Published: October 2019

Pruritus is one of the most common dermatologic complaints and, as the most common dermatologic symptom, is a major contributor to frequent dermatology visits. Chronic pruritus mirrors another major medical condition faced by millions of Americans each year ‐ chronic pain. In older literature, pain and pruritus were thought to have been conveyed by the same C fiber, and the proportion contributing to pruritus was just a small subset of this general fiber. Overall, pain and pruritus share many integral similarities. Although these sensations both initiate the body’s awareness to injury, pain and itch may have evolved for sensing different damages such as a burrowing parasite or a noxious stimulus, respectively. This seems to have been validated through analyses of their pathophysiology, acute and chronic conditions, and treatment modalities. However, their symptoms and intrinsic mechanisms vary considerably. It is important to view pruritus in more of an overall, whole body experience, rather than just the sensory aspect. Future studies should investigate the psychological treatment of chronic pruritus, considering the immense similarities with its chronic pain counterpart.
Fast and fierce versus slow and smooth: Heterogeneity in immune responses to Plasmodium in the controlled human malaria infection model
Authors: Yap Xi Zen , McCall Matthew B. B. , Sauerwein Robert W.
Published: October 2019

Controlled human malaria infection (CHMI) is an established model in clinical malaria research. Upon exposure to Plasmodium falciparum parasites, malaria‐naive volunteers differ in dynamics and composition of their immune profiles and subsequent capacity to generate protective immunity. CHMI volunteers are either inflammatory responders who have prominent cellular IFN‐γ production primarily driven by adaptive T cells, or tempered responders who skew toward antibody‐mediated humoral immunity. When exposed to consecutive CHMIs under antimalarial chemoprophylaxis, individuals who can control parasitemia after a single immunization (fast responders) are more likely to be protected against a subsequent challenge infection. Fast responders tend to be inflammatory responders who can rapidly induce long‐lived IFN‐γ+ T cell responses. Slow responders or even non‐responders can also be protected, but via a more diverse range of responses that take a longer time to reach full protective efficacy, in part due to their tempered phenotype. The latter group can be identified at baseline before CHMI by higher expression of inhibitory ligands CTLA‐4 and TIM‐3 on CD4+ T cells. Delineating heterogeneity in human immune responses to P. falciparum will facilitate rational design and strategy towards effective malaria vaccines.
Holocene increases in palm abundances in north‐western Amazonia
Authors: Heijink Britte M. , McMichael Crystal N. H. , Piperno Dolores R. , Duivenvoorden Joost F. , Cárdenas Dairon , Duque Álvaro
Published: October 2019

Aim

In Amazonia, 227 of c. 16,000 tree species account for half the individual trees (termed ‘hyperdominant’ species), and a disproportionate number of these species are palms. Our objectives are to show how and whether palm abundance has changed through the Holocene. Here, we reconstruct a detailed fire and vegetation history from north‐western Amazonia, with a focus on changes in palm abundances, and compare our results with regional data.

Location

Amacayacu, Colombia.

Taxon

Amazonian palms.

Methods

We performed charcoal and phytolith analysis on soil cores, and obtained ages of past fires using 14C dating. We measured charcoal abundances and the relative abundances of phytoliths (silica‐based microfossils) for all samples. We used these data to reconstruct changes in fire and vegetation, and compared these data with the species composition of palms in the modern forest.

Results

Seven 14C dates from charcoal in three cores provided fire ages ranging from 1630 to 2450 calibrated years before present. Charcoal was absent from one‐third of the cores. Palm phytoliths from genera such as Iriartea, Socratea, and Astrocaryum have increased through time, while genera such as Euterpe, Hyospathe, and Oenocarpus have remained relatively stable and similar to modern levels. Overall, palm abundances were negatively correlated with charcoal measurements. Decorated sphere phytoliths, produced from unknown arboreal taxa were positively correlated with charcoal presence and abundance.

Main conclusions

Palms have increased at Amacayacu and other forest plots through time, but the increases are largest in north‐western Amazonia. The presence of fire, however, dampens the increase in palms through time. When compared with reconstructions from other Amazon regions, our results suggest that increases in palm abundances in the late Holocene occurred both in the presence and absence of direct pre‐Columbian human influence, and that response was strongest in north‐western Amazonia when human influence was minimal.
Improvement of urban flood damage estimation using a high‐resolution digital terrain
Authors: Kim Young Do , Tak Yong Hun , Park Mun Hyun , Kang Boosik
Published: October 2019

Because urban flooding occurs frequently, it is important to calculate the areal extent of flooding based on flood volumes and water levels, and thus, the extent of expected damage can be effectively estimated. In this study, urban inundation from heavy rainfall and the contribution of topographic scales to urban river drainage basins in Seoul, Korea are simulated. A light detection and ranging (LiDAR)‐based 1× 1 m digital elevation model (DEM) and a 1:5,000 digital map‐based 10 × 10 m DEM are used in this study for the storm water management model (SWMM). Using a multi‐dimensional flood damage analysis to estimate economic damage, the asset value of each building type is analyzed in connection with the construction cost of buildings, household ratio, and building area, and then, the building damage is calculated at each flood level based on the percentage of building damage. Based on the analysis, 119.6 and 55.8 M USD in damages are expected to occur according to the 1 and 10 m DEMs, respectively. The results of this study can be used to evaluate alternatives for urban flooding mitigation and an optimal mitigation measure can be suggested among the alternatives because the methods used for predicting floods are examined and the associated damages are accurately estimated using digital terrain data at precise scales.
The Caregiver Burden of Delirium in Older Adults With Alzheimer Disease and Related Disorders
Authors: Fong Tamara G. , Racine Annie M. , Fick Donna M. , Tabloski Patricia , Gou Yun , Schmitt Eva M. , Hshieh Tammy T. , Metzger Eran , Bertrand Sylvie E. , Marcantonio Edward R. , Jones Richard N. , Inouye Sharon K.
Published: October 2019

OBJECTIVES

To measure the burden of delirium in older adults with or without Alzheimer disease or related disorders (ADRDs).

DESIGN

Prospective, observational cohort.

SETTING

Inpatient hospital and study participants' homes.

PARTICIPANTS

A subset (n = 267) of older medical and surgical patients and their caregivers enrolled in the Better Assessment of Illness study.

MEASUREMENTS

Delirium burden was measured using the DEL‐B instrument (range = 0‐40, with higher scores indicating greater burden) in caregivers (DEL‐B‐C) and patients 1 month after hospitalization. Severity of cognitive impairment (Montreal Cognitive Assessment [MoCA]), delirium presence (Confusion Assessment Method [CAM]), and delirium severity (CAM‐Severity [CAM‐S]) were measured during hospitalization and at 1‐month follow‐up. ADRD diagnosis was determined by a clinical consensus process.

RESULTS

For patients with (n = 56) and without (n = 211) ADRD, both DEL‐B instruments had good internal consistency. DEL‐B‐C scores had a median (interquartile range) among caregivers of patients with and without ADRD of 9 (5‐15) and 5 (1‐11), respectively (P < .05). If the patient developed delirium, caregivers experienced greater burden (β[delirium × ADRD] = −.29; P = .42), regardless of ADRD status. Further, caregiver burden was modestly correlated with patient MoCA scores (Spearman correlation coefficient, ρ = −0.18; P = .01). Patients with ADRD who developed delirium self‐reported less burden than those without ADRD (β[delirium × ADRD] = −.67; P = .044). As with caregivers, delirium burden was modestly correlated with patient MoCA score (ρ = −0.18; P = .005) and correlated with the CAM‐S in patients without ADRD (ρ = 0.38; P < .001) but not for patients with ADRD (ρ = −0.07; P = .61).

CONCLUSIONS

Delirium resulted in the same degree of increased caregiver burden regardless of whether a patient had ADRD, signifying delirium is equally stressful to caregivers, even among those with experience caring for someone with a chronic cognitive disorder. Delirium burden is only modestly associated with degree of cognitive impairment, suggesting that other aspects of delirium contribute to burden. J Am Geriatr Soc 67:2587–2592, 2019