bluuebunny/crossref_metadata_2025 huggingface dataset:
The phylogeny of insects in the data‐driven era
Authors: Chesters Douglas
Published: December 2019

Maturation of omics and DNA barcode programs along with advances in sequence analysis tools and phyloinformatics protocols are enabling the realization of comprehensive and robust phylogenies of even the most diverse lineages. Several lineages in insects have undergone hyper‐radiations, and thus a unified picture of their evolution is ultimately required for understanding the process of diversification. In this study I further develop informatics protocols for de novo phylogenetic construction, and present the most species‐comprehensive insect phylogeny to date, constructed hierarchically using c. 440 transcriptomes, 1490 mitogenomes, DNA barcodes for 69 000 species, and several additional species‐rich markers. Even with this expanded transcriptome backbone, support is still insufficient for some historically problematic nodes, particularly in Polyneoptera and Paraneoptera. Low support (measured by internode certainty) was observed for the node separating Dictyoptera from its sister polyneopeterans; configuration of the Paraneoptera was not resolved; the recently proposed Hymenoptera grouping Eusymphyta received high support, while Parasitoida did not; and Orthorrhapha (Diptera) was not recovered. Sampling is uneven across the insects, and while highly sequenced lineages (e.g. Lepidoptera) boast greater information content, this accompanies computational burdens. The protocol and resulting tree represent an advance in the analytic and phylogenetic framework, for an objectively and consistently determined species‐comprehensive phylogeny.
The Ethical Consequences of Criminalizing Solidarity in the EU
Authors: Duarte Melina
Published: December 2019

The aftermath of the European refugee crisis can be said to have sparked a crisis of solidarity. Despite abundant demonstrations of solidarity with refugees and asylum seekers, what many saw as an exercise of their duty to help was made illegal. The critical term that emerged to refer to this conjuncture was “criminalization of solidarity”. In order to include this term in the academic debate, this article starts by disclosing the embedded claims present in its rhetorical usage. The article then scrutinizes the design of the politics of criminalizing solidarity and its consequences. It argues that at least three aspects of the politics of criminalizing solidarity plausibly indicate the possibility that regulating the aid in question will produce and reinforce consequences for the EU that are not only unintended, but also damaging. This is because, first, what I refer to as the blending aspect might spread the perception of illegality among several types of immigrants; second, the moral aspect can discharge people from their duty to help foreigners by conditioning this duty to group membership and belonging; and third, the polarizing aspect might exacerbate the existing divide between citizens and immigrants currently causing conflicts and social fragmentation.
PEROXIREDOXIN Q stimulates the activity of the chloroplast 16:1Δ3trans FATTY ACID DESATURASE4
Authors: Horn Patrick J. , Smith Montgomery D. , Clark Tessa R. , Froehlich John E. , Benning Christoph
Published: December 2019

Thylakoid membrane lipids, comprised of glycolipids and the phospholipid phosphatidylglycerol (PG), are essential for normal plant growth and development. Unlike other lipid classes, chloroplast PG in nearly all plants contains a substantial fraction of the unusual trans fatty acid 16:1Δ3trans or 16:1t. We determined that, in Arabidopsis thaliana, 16:1t biosynthesis requires both FATTY ACID DESATURASE4 (FAD4) and a thylakoid‐associated redox protein, PEROXIREDOXIN Q (PRXQ), to produce wild‐type levels of 16:1t. The FAD4–PRXQ biochemical relationship appears to be very specific in planta, as other fatty acids (FA) desaturases do not require peroxiredoxins for their activity, nor does FAD4 require other chloroplast peroxiredoxins under standard growth conditions. Although most of chloroplast PG assembly occurs at the inner envelope membrane, FAD4 was primarily associated with the thylakoid membranes facing the stroma. Furthermore, co‐production of PRXQ with FAD4 was required to produce Δ3‐desaturated FAs in yeast. Alteration of the redox state of FAD4 or PRXQ through site‐directed mutagenesis of conserved cysteine residues impaired Δ3 FA production. However, these mutations did not appear to directly alter disulfide status of FAD4. These results collectively demonstrate that the production of 16:1t is linked to the redox status of the chloroplast through PRXQ associated with the thylakoids.
Hidden value in the platform’s platform: Airbnb, displacement, and the un‐homing spatialities of emotional labour
Authors: Spangler Ian
Published: December 2019

This paper explores the proliferation of short‐term home rentals (STRs) in New Orleans, Louisiana, USA, to consider how contemporary technologies of platform urbanism leverage the human infrastructure of emotional labour as a technique for value production. Bringing theories of emotional labour and gentrification together with recent writing on the spatialities of platforms, I argue that for the production of value and the capture of profit, STR platforms like Airbnb rely on neighbours’ emotional labour of performing home. Because this strategy operates through banal practices in quite ordinary neighbourhood spaces, it hides in plain sight – and yet, for neighbours who find themselves enrolled without remuneration into the productive machinery of platform capitalism, it simultaneously creates feelings of alienation and exhaustion. Drawing on interviews with neighbourhood residents and Airbnb hosts in New Orleans, I show how neighbours’ unremunerated performances of home contribute to their own feelings of displacement in place while simultaneously operating as an apparatus of value production for the platform. Although I focus on the case of Airbnb in New Orleans, this study also broadly demonstrates the invisibilisation of value, the challenges of opting out of the digital economy, and the embodied ways in which relations of platform urbanism can impact the everyday life of people with no formal obligation to platforms themselves.
Development justice, a proposal: Reckoning with disaster, catastrophe, and climate change in the Caribbean
Authors: Gahman Levi , Thongs Gabrielle
Published: December 2019

This paper proposes that “development justice” be taken up as an analytical concept and praxis‐driven framework for research on disasters, resilience, and climate change. The piece begins with a synopsis of the historical‐structural factors exacerbating risk in the Caribbean before reviewing the concepts of vulnerability, resilience, and development justice. Next, drawing from empirical data and via a development justice lens, we highlight how the logics, practices, and debts of colonial underdevelopment, racial capitalism, and neoliberal extraction continue to erode resilience across the region. We end by recommending that future adaptation and mitigation strategies related to disasters, catastrophes, and climate change be more attentive to structural and slow violence, as well as the historical trajectories of imperialism, racial capitalism, and hetero patriarchal norms. In sum, the piece constitutes an evidence‐based assertion that development justice perspectives alongside theories of non‐metaphorical decolonisation be used by scholars, activists, scientists, and states alike who are committed to mediating climate change and preventing/reducing the damage caused by disasters.
Successful management of Heinz body hemolytic anemia associated with leek (Allium ampeloprasum) ingestion in a South American coati (Nasua nasua)
Authors: Jayson Stephanie , Masters Nic , Strike Taina , Rendle Matthew , Sparrow Sophie , Peters Laureen M. , Bates Nicola
Published: December 2019

Objective

To describe the diagnosis, management, and outcome of Heinz body hemolytic anemia in a South American coati (Nasua nasua) secondary to suspected leek (Allium ampeloprasum) toxicosis.

Case Summary

A South American coati presented with Heinz body hemolytic anemia following addition of leeks to its diet for 2–5 days prior to initial presentation. Administration of a whole blood transfusion from an animal of the same species (conspecific) and supportive care resulted in immediate improvement in clinical signs. Normal behavior fully returned within 6 days of transfusion. Hematological evidence of anemia resolved by 4 weeks and there were no significant features of oxidative injury present by 8 weeks following initial presentation.

New Information Provided

This is the first reported case of Heinz body hemolytic anemia, suspected leek toxicosis, and administration of a blood transfusion in this species.
Determinants of the diminished exercise capacity in patients with chronic obstructive pulmonary disease: looking beyond the lungs
Authors: Broxterman Ryan M. , Hoff Jan , Wagner Peter D. , Richardson Russell S.
Published: December 2019

Key points

Peak oxygen uptake, a primary determinant of prognosis, mortality and quality of life, is diminished in patients with chronic obstructive pulmonary disease (COPD), with mounting evidence supporting an important role for peripheral dysfunction, particularly within skeletal muscle.

In patients with severe COPD and activity‐matched controls, muscle oxygen transport and utilization were assessed at peak effort during single‐leg knee‐extensor exercise (KE), where ventilation is assumed to be submaximal. This strategy removes ventilation as the major constraint to exercise capacity in COPD, allowing maximal muscle function to be attained and evaluated.

During maximal KE, both convective arterial oxygen delivery to the skeletal muscle microvasculature and subsequent diffusive oxygen delivery to the mitochondria were diminished in patients with COPD compared to control subjects.

These findings emphasize the importance of factors, beyond the lungs, that influence exercise capacity in this patient population and may, ultimately, influence the prognosis, mortality and quality of life for patients with COPD.

Peak oxygen uptake (), a primary determinant of prognosis, mortality and quality of life, is diminished in patients with chronic obstructive pulmonary disease (COPD). Mounting evidence supports an important role of the periphery, particularly skeletal muscle, in the diminished with COPD. However, the peripheral determinants of have not been comprehensively assessed in this cohort. Thus, the hypothesis was tested that both muscle convective and diffusive oxygen (O2) transport, and therefore skeletal muscle peak O2 uptake (), are diminished in patients with COPD compared to matched healthy controls, even when ventilatory limitations (i.e. attainment of maximal ventilation) are minimized by using small muscle mass exercise. Muscle O2 transport and utilization were assessed at peak exercise from femoral arterial and venous blood samples and leg blood flow (by thermodilution) in eight patients with severe COPD (forced expiratory volume in 1s (FEV1) ± SEM = 0.9 ± 0.1 l, 30% of predicted) and eight controls during single‐leg knee‐extensor exercise. Both muscle convective O2 delivery (0.44 ± 0.06 vs. 0.69 ± 0.07 l min−1, P < 0.05) and muscle diffusive O2 conductance (6.6 ± 0.8 vs. 10.4 ± 0.9 ml min−1 mmHg−1, P < 0.05) were ∼1/3 lower in patients with COPD than controls, resulting in an attenuated in the patients (0.27 ± 0.04 vs. 0.42 ± 0.05 l min−1, P < 0.05). When cardiopulmonary limitations to exercise are minimized, the convective and diffusive determinants of , at the level of the skeletal muscle, are greatly attenuated in patients with COPD. These findings emphasize the importance of factors, beyond the lungs, that may ultimately influence this population's prognosis, mortality and quality of life.
Uma abordagem sobre a aplicação da Teoria da Resposta ao Item nas avaliações de aprendizagem do ensino contábil brasileiro
Authors: Corrêa da Silva Maurício , Bernardes do Nascim João Carlos Hipólito , Gomes da Silva José Dionísio , Maia de Siqueira José Ricardo
Published: December 2019

O presente estudo discute as contribuições da aplicação da Teoria da Resposta ao Item ­–TRI– nas avaliações de aprendizagem do ensino contábil brasileiro. A TRI possibilita a estimação, além da habilidade do respondente, dos parâmetros de dificuldade, discriminação e acertos casuais de cada item. Como resultado das discussões teóricas, notou-se que, entre os principais benefícios provenientes da aplicação da TRI no ensino contábil, destacam-se: o desenvolvimento de avaliações que capturam os parâmetros dos itens; a elaboração de bancos de itens que possibilitará a aplicação de provas equivalentes em datas distintas, a identificação de itens enviesados evitará problemas de injustiça social e a equiparação de escores proporcionará uma avaliação comparativa mais adequada. Assim, os artigos analisados justificam a abordagem da aplicação da técnica da TRI nas avaliações de aprendizagem do ensino contábil brasileiro pelos elementos problematizados na formação pedagógica dos docentes do Curso de Graduação em Ciências Contábeis.
Competitividad de las Pyme y su relación con los sistemas de información
Authors: Saavedra García María Luisa , Camarena Adame María Elena , Saavedra García Miriam Edith
Published: December 2019

El objetivo de esta investigación consiste en determinar si existe una relación entre los sistemas de información y la competitividad de las Pyme en la Ciudad de México. Se utilizaron los resultados de un estudio previo realizado por Saavedra (2014), en el que se recolectaron datos en una muestra de 400 Pyme. Con estos datos se realizó un análisis descriptivo y correlacional. Los principales hallazgos muestran que la implementación de sistemas de información es incipiente. Sin embargo, existe una relación significativa de la competitividad de las Pyme con todos los factores de sistemas de información, y de estos con las Pyme de tamaño micro y pequeñas. Igualmente, se muestra una relación significativa entre dichos factores y los sectores de comercio y servicios de las Pyme. Estos hallazgos corroboran lo encontrado en la literatura previa.
Influência das características organizacionais na evidenciação de diferentes categorias de custos ambientais
Authors: Krein Viviane , Koprowski Sirlene , Zanin Antonio , Mazzioni Sady , Baú Dal Magro Cristian
Published: December 2019

O objetivo do artigo é analisar a influência das características organizacionais na evidenciação de diferentes categorias de custos ambientais nas empresas brasileiras de capital aberto listadas na bolsa de valores do Brasil (B3). Para determinar o nível de evidenciação dos custos ambientais adotou-se a fração entre as expressões-chave e a quantidade de páginas, constantes nos relatórios de sustentabilidade divulgados pelas organizações em questão, referentes a 2017. Os achados indicam que o nível médio de evidenciação de informações sobre custos ambientais das empresas pesquisadas é de 24,90%. A categoria mais evidenciada é custos para controlar a ocorrência de impactos ambientais (14,70%). Conclui-se que a característica de tamanho organizacional exerce influência positiva nos níveis de evidenciação em todas as categorias; pertencer ao Índice de Sustentabilidade Empresarial, ser internacionalizada e ter uma auditoria big four melhoram a evidenciação acima mencionada; enquanto níveis mais elevados de governança corporativa estão relacionados com uma menor evidenciação.
Complementary description of Africoseius lativentris and placement of Africoseius in Podocinidae (Acari, Mesostigmata) based on molecular and morphological evidences

Authors: Rueda-Ramírez Diana , Santos Jandir C. , Sourassou Nazer Famah , Demite Peterson R. , Puerta-gonzález Andrés , De Moraes Gilberto J.
Published: December 2019

Morphological details of specimens collected from several localities in Brazil and identified as Africoseius lativentris (Karg 1982) are provided. The taxonomic position of Africoseius Krantz, 1962 has been debated over the years, with repeated changes in its familial placement. A phylogenetic study based on 18S and 28S rDNA sequences of the Brazilian population of A. lativentris collected at Jaboticabal, São Paulo State, and similar data of 70 taxa representing 11 families of Gamasina indicated that Africoseius is a member of the well-supported Podocinidae (sensu Lindquist et al. 2009) clade. The main morphological similarities and differences between Africoseius and the group of species until now placed in Podocinidae sensu Lindquist et al. (2009) are listed. Apomorphic characteristics uniting those taxa include the hypotrichous condition of tibia I (eight and nine setae instead of ten or more in other free-living Gamasina) and the insertions of av2 and pv2, considerably more distal on tarsi II and III than in the majority of the free-living Gamasina. Within Podocinidae, a new subfamily, Africoseiinae, is proposed, based on uniquely apomorphic characteristics of the setae ad4 and pd4 (sensu  Evans 1969) of tarsi II–IV absent, and setae av4 and pv4 of same basitarsi long, incurved and close to each other and to a posterior longitudinal extension of the peripodomeric suture and on the attenuated form of the lateral (rather than the medial) hypostomatic setae. This subfamily is currently represented by Africoseius areolatus Krantz and Africoseius lativentris (Karg 1982), while all other presently known species of the family are now placed in the subfamily Podocininae.
Molecular and ontogeny studies clarify systematic status of Chamobates borealis (Acari, Oribatida, Chamobatidae): an integrated taxonomy approach

Authors: Seniczak Anna , Seniczak Stanisław , Jordal Bjarte H.
Published: December 2019

Chamobates borealis (Trägårdh 1902) has been considered by some authors as a junior synonym of Chamobates pusillus (Berlese 1895). In this study we used an integrated taxonomy approach, comparing mitochondrial coding gene COI and morphological ontogeny of these species to clarify their systematic status. The Bayesian inference tree based on COI sequences of C. borealis and C. pusillus, as well as C. birulai (Kulczyński 1902), C. bispinosus Mahunka, 1987, C. cuspidatus (Michael 1884) and C. rastratus (Hull 1914) separated all these species. In terms of the morphology, the adults of C. borealis and C. pusillus have similar body size and shape, thin aggenital setae and two lateral teeth on the rostrum, but C. borealis has the medial incision between these teeth, which is absent in C. pusillus. The adults of these species differ also from each other by the shape of bothridial setae, size of area porose Aa, location of seta lm and lyrifissure im, and the shape of most setae on the hysterosoma. The morphological ontogeny of these species is similar, but the larva and nymphs of C. borealis differ from those of C. pusillus by the length of some prodorsal and gastronotal setae, and the nymphs of C. borealis have a humeral organ, which is absent in C. pusillus. The presence of a humeral organ in some Chamobates species supports a clade inferred by COI sequence data.
Transmission Mueller-matrix characterization of transparent ramie films
Authors: Mendoza-Galván Arturo , Li Yuanyuan , Yang Xuan , Magnusson Roger , Järrendahl Kenneth , Berglund Lars , Arwin Hans
Published: December 2019

Ramie is a plant whose fibers are used in fabrics. Ramie films are prepared by hot pressing and studied with transmission Mueller-matrix ellipsometry, which provides a complete description of polarizing and depolarizing sample properties. Symmetries of the Mueller matrices imply that the ramie films are linearly birefringent and act as waveplates. The linear birefringence is quantified by the differential decomposition of the Mueller matrices and the materials’ birefringence is found to be of the order of 0.05–0.08 with small dispersion in the visible spectral range. The films exhibit depolarization, which is quantified in terms of the depolarization index and varies from 0.9 in the infrared to 0.25 in the ultraviolet range. The deep understanding of ramie films’ polarization properties will pave the way for applications in optical and photonic devices.
Excitation of moderate-frequency Love wave in a Plexiglas plate on aluminum semi-space
Authors: Chen Mingtong , Huan Qiang , Li Faxin
Published: December 2019

Love waves are of great importance in geophysics, electronics, and engineering. Despite intensive studies on high-frequency Love waves for delay lines and chemical/biomedical sensors, moderate-frequency and low-frequency Love waves have seldom been investigated. Here, Love waves in a 2-mm-thick Plexiglas plate bonded on a 50-mm-thick aluminum block were successfully excited and received by using d24 and d15 shear mode PZT wafers. A d31 mode PZT wafer was also employed as the sensor, and results show that no Rayleigh-Lamb type waves were generated. The group velocity curve of the excited Love wave from 120 to 525 kHz matches the theoretical curve well. This work could promote applications of Love waves in many engineering fields.
Range of Yoga Intensities From Savasana to Sweating: A Systematic Review
Authors: Forseth Bethany , Hunter Stacy D.
Published: December 2019

Background: There is limited research examining the intensity of yoga and intensity variations between different styles. The purpose of this review is to examine the intensity of yoga based on different physiologic responses both between different yoga styles and within styles of yoga. Methods: Articles were searched for on the PubMed database in early 2019. Inclusion criteria were as follows: (1) written in English, (2) cite a specific style of yoga and include whole yoga session, and (3) measure metabolic or heart rate response. Results: Ten articles were reviewed; articles reported oxygen consumption (n = 1), heart rate (n = 4), or both variables (n = 5). Yoga styles assessed included ashtanga (n = 2), Bikram (n = 3), gentle (n = 1), hatha (n = 3), Iyengar (n = 1), power (n = 1), and vinyasa (n = 1). Oxygen consumption commonly categorized yoga as a light-intensity activity, while heart rate responses classified different yoga into multiple intensities. Conclusion: This review demonstrates that large differences in intensity classifications are observed between different styles of yoga. Furthermore, metabolic and heart rate responses can be variable, leading to inconsistent intensity classifications. This is likely due to their nonlinear relationship during yoga. Thus, it is imperative that the field of yoga research works together to create a standard for reporting yoga.
Direct single-molecule quantification reveals unexpectedly high mechanical stability of vinculin—talin/α-catenin linkages
Authors: Le Shimin , Yu Miao , Yan Jie
Published: December 2019

Single-molecule manipulation reveals high mechanical stability of vinculin—talin and vinculin—α-catenin protein-protein interfaces.
ATAT1-enriched vesicles promote microtubule acetylation via axonal transport
Authors: Even Aviel , Morelli Giovanni , Broix Loïc , Scaramuzzino Chiara , Turchetto Silvia , Gladwyn-Ng Ivan , Le Bail Romain , Shilian Michal , Freeman Stephen , Magiera Maria M. , Jijumon A. S. , Krusy Nathalie , Malgrange Brigitte , Brone Bert , Dietrich Paula , Dragatsis Ioannis , Janke Carsten , Saudou Frédéric , Weil Miguel , Nguyen Laurent
Published: December 2019

The axonal transport of vesicles promotes microtubule acetylation across species.
Illuminating subduction zone rheological properties in the wake of a giant earthquake
Authors: Weiss Jonathan R. , Qiu Qiang , Barbot Sylvain , Wright Tim J. , Foster James H. , Saunders Alexander , Brooks Benjamin A. , Bevis Michael , Kendrick Eric , Ericksen Todd L. , Avery Jonathan , Smalley Robert , Cimbaro Sergio R. , Lenzano Luis E. , Barón Jorge , Báez Juan Carlos , Echalar Arturo
Published: December 2019

We invert postseismic geodetic data to reveal subduction zone mechanical properties following a megathrust earthquake in Chile.
Extreme Zr stable isotope fractionation during magmatic fractional crystallization
Authors: Ibañez-Mejia Mauricio , Tissot François L. H.
Published: December 2019

Zr stable isotopes exhibit >5‰ fractionations at magmatic conditions, yielding novel insights into melt chemical evolution.
Direct conversion of carlactonoic acid to orobanchol by cytochrome P450 CYP722C in strigolactone biosynthesis
Authors: Wakabayashi Takatoshi , Hamana Misaki , Mori Ayami , Akiyama Ryota , Ueno Kotomi , Osakabe Keishi , Osakabe Yuriko , Suzuki Hideyuki , Takikawa Hirosato , Mizutani Masaharu , Sugimoto Yukihiro
Published: December 2019

P450 CYP722C is a key enzyme catalyzing orobanchol synthesis and orobanchol is undetectable in root exudates after gene knockout.
The long noncoding RNA
neuroLNC
regulates presynaptic activity by interacting with the neurodegeneration-associated protein TDP-43
Authors: Keihani S. , Kluever V. , Mandad S. , Bansal V. , Rahman R. , Fritsch E. , Gomes L. Caldi , Gärtner A. , Kügler S. , Urlaub H. , Wren J. D. , Bonn S. , Rizzoli S. O. , Fornasiero E. F.
Published: December 2019

NeuroLNC
, a previously unknown long ncRNA, regulates neuronal activity by interacting with the neurodegeneration protein TDP-43.
Population dynamics modify urban residents’ exposure to extreme temperatures across the United States
Authors: Yang Jiachuan , Hu Leiqiu , Wang Chenghao
Published: December 2019

Daily commute substantially increases urban residents’ exposure to heat waves and slightly alleviates exposure to cold waves.
High-throughput evolution of near-infrared serotonin nanosensors
Authors: Jeong Sanghwa , Yang Darwin , Beyene Abraham G. , Del Bonis-O’Donnell Jackson Travis , Gest Anneliese M. M. , Navarro Nicole , Sun Xiaoqi , Landry Markita P.
Published: December 2019

Synthetic near-infrared nanosensors are evolved for imaging neuromodulator serotonin with high spatiotemporal resolution.
A formal methods approach to interpretable reinforcement learning for robotic planning
Authors: Li Xiao , Serlin Zachary , Yang Guang , Belta Calin
Published: December 2019

A formal methods approach to reinforcement learning generates rewards from a formal language and guarantees safety.
A Novel
d
-Allulose 3-Epimerase Gene from the Metagenome of a Thermal Aquatic Habitat and
d
-Allulose Production by Bacillus subtilis Whole-Cell Catalysis
Authors: Patel Satya Narayan , Kaushal Girija , Singh Sudhir P.
Published: December 2019

d
-Allulose is a noncaloric sugar substitute with antidiabetes and antiobesity potential. With several characteristics of physiological significance,
d
-allulose has wide-ranging applications in the food and pharmacology industries. The development of a thermostable biocatalyst is an objective of mainstream research aimed at achieving industrial acceptability of the enzyme. Aquatic habitats of extreme temperatures are considered a potential metagenomic resource of heat-tolerant biocatalysts of industrial importance. The present study explored the thermal-spring metagenome of the Tattapani geothermal region, Chhattisgarh, India, discovering a novel
d
-allulose 3-epimerase gene,
daeM
, encoding an enzyme of high-level heat stability. The
daeM
gene was expressed in the microbial cells of a nonpathogenic and safe-grade species,
B. subtilis
, which was found to be capable of performing
d
-fructose to
d
-allulose interconversion via a whole-cell catalysis reaction. The results indicate that DaeM is a potential biocatalyst for commercial production of the rare sugar
d
-allulose. The study established that extreme environmental niches represent a genomic resource of functional sugar-related biocatalysts.
Initial Reductive Reactions in Aerobic Microbial Metabolism of 2,4,6-Trinitrotoluene
Authors: Vorbeck Claudia , Lenke Hiltrud , Fischer Peter , Spain Jim C. , Knackmuss Hans-Joachim
Published: December 2019

Because of its high electron deficiency, initial microbial transformations of 2,4,6-trinitrotoluene (TNT) are characterized by reductive rather than oxidation reactions. The reduction of the nitro groups seems to be the dominating mechanism, whereas hydrogenation of the aromatic ring, as described for picric acid, appears to be of minor importance. Thus, two bacterial strains enriched with TNT as a sole source of nitrogen under aerobic conditions, a gram-negative strain called TNT-8 and a gram-positive strain called TNT-32, carried out nitro-group reduction. In contrast, both a picric acid-utilizing
Rhodococcus erythropolis
strain, HL PM-1, and a 4-nitrotoluene-utilizing
Mycobacterium
sp. strain, HL 4-NT-1, possessed reductive enzyme systems, which catalyze ring hydrogenation, i.e., the addition of a hydride ion to the aromatic ring of TNT. The hydride-Meisenheimer complex thus formed (H
−
-TNT) was further converted to a yellow metabolite, which by electrospray mass and nuclear magnetic resonance spectral analyses was established as the protonated dihydride-Meisenheimer complex of TNT (2H
−
-TNT). Formation of hydride complexes could not be identified with the TNT-enriched strains TNT-8 and TNT-32, or with
Pseudomonas
sp. clone A (2NT
−
), for which such a mechanism has been proposed. Correspondingly, reductive denitration of TNT did not occur.
Stable-Carbon-Isotope Composition of Fatty Acids in Hydrothermal Vent Mussels Containing Methanotrophic and Thiotrophic Bacterial Endosymbionts
Authors: Pond David W. , Bell Michael V. , Dixon David R. , Fallick Anthony E. , Segonzac Michel , Sargent John R.
Published: December 2019

Fatty acid biomarker analysis coupled with gas chromatography-isotope ratio mass spectrometry was used to confirm the presence of methanotrophic and thiotrophic bacterial endosymbionts in the tissues of a hydrothermal vent mussel (
Bathymodiolus
sp.), collected from the Menez Gwen vent field on the mid-Atlantic ridge. Monounsaturated (n-8) fatty acids, which are diagnostic of methanotrophic bacteria, were detected in all three types of tissues examined (gill, posterior adductor, and mantle), although levels were highest in gill tissues where the bacteria were found. Stable-carbon-isotope compositions (δ-
13
C per mille relative to that of Peedee belemnite) of fatty acids for all three tissues ranged from −24.9 to −34.9‰, which encompasses the range predicted for both thiotroph- and methanotroph-based nutrition. The data suggest that these thio- and methanotrophic bacterial endosymbionts are equally important in the nutrition of the vent mussel at this particular vent site.
Purification and Properties of ArfI, an α-
l
-Arabinofuranosidase from
Cytophaga xylanolytica
Authors: Renner Michael J. , Breznak John A.
Published: December 2019

An α-
l
-arabinofuranosidase (α-
l
-arabinofuranoside arabinofuranohydrolase [EC
3.2.1.55
]; referred to below as ArfI) from
Cytophaga xylanolytica
XM3 was purified 85-fold by anion-exchange and hydrophobic interaction column chromatography. The native enzyme had a pI of 6.1 and an apparent molecular mass of 160 to 210 kDa, and it appeared to be a trimer or tetramer consisting of 56-kDa subunits. With
p
-nitrophenyl-α-
l
-arabinofuranoside as the substrate, the enzyme exhibited a

K
m

of 0.504 mM and a
V
max
of 319 μmol · min
−1
· mg of protein
−1
, and it had optimum activity at pH 5.8 and 45°C. ArfI was relatively stable over a pH range of 4 to 10 and at temperatures up to 45°C, and it retained nearly full activity when stored at 4°C for periods as long as 24 months. The enzyme also released arabinose from 4-methylumbelliferyl-α-
l
-arabinofuranoside, as well as from rye, wheat, corn cob, and oat spelt arabinoxylans and sugar beet arabinan, but not from arabinogalactan. ArfI showed no hydrolytic activity toward a range of
p
-nitrophenyl- or 4-methylumbelliferyl-glycosides other than arabinoside, for which it was entirely specific for the α-
l
-furanoside configuration. ArfI interacted synergistically with three partially purified endoxylanase fractions from
C. xylanolytica
in hydrolyzing rye arabinoxylan. However, cell fractionation studies revealed that ArfI was largely, if not entirely, cytoplasmic, so its activity in vivo is probably most relevant to hydrolysis of arabinose-containing oligosaccharides small enough to pass through the cytoplasmic membrane. Antibodies prepared against purified ArfI also cross-reacted with arabinofuranosidases from other freshwater and marine strains of
C. xylanolytica
, as well as with some proteins that did not possess arabinofuranosidase activity. To our knowledge, this is the first α-
l
-arabinofuranosidase to be purified and characterized from any gliding bacterium.
IS
D1
, an Insertion Element from the Sulfate-Reducing Bacterium
Desulfovibrio vulgaris
Hildenborough: Structure, Transposition, and Distribution
Authors: Fu Rongdian , Voordouw Gerrit
Published: December 2019

Insertion element IS
D1
, discovered when its transposition caused the insertional inactivation of an introduced
sacB
gene, is present in two copies in the genome of
Desulfovibrio vulgaris
Hildenborough. Southern blot analysis indicated at least two insertion sites in the
sacB
gene. Cloning and sequencing of a transposed copy of IS
D1
indicated a length of 1,200 bp with a pair of 44-bp imperfect inverted repeats at the ends, flanked by a direct repeat of the 4-bp target sequence. AAGG and AATT were found to function as target sequences. IS
D1
encodes a transposase from two overlapping open reading frames by programmed translational frameshifting at an A
6
G shifty codon motif. Sequence comparison showed that IS
D1
belongs to the IS
3
family. Isolation and analysis of the chromosomal copies, IS
D1
-A and IS
D1
-B, by PCR and sequencing indicated that these are not flanked by direct repeats. IS
D1
-A is inserted in a region of the chromosome containing the
gapdh-pgk
genes (encoding glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase). Active transposition to other loci in the genome was demonstrated, offering the potential of a new tool for gene cloning and mutagenesis. IS
D1
is the first transposable element described for the sulfate reducers, a large and environmentally important group of bacteria. The distribution of IS
D1
in genomes of sulfate-reducing bacteria is limited. A single copy is present in the genome of
D. desulfuricans
Norway.
Manganese Peroxidase-Dependent Oxidation of Glyoxylic and Oxalic Acids Synthesized byCeriporiopsis subvermisporaProduces Extracellular Hydrogen Peroxide
Authors: Urzúa Ulises , Kersten Philip J. , Vicuña Rafael
Published: December 2019

The ligninolytic system of the basidiomyceteCeriporiopsis subvermisporais composed of manganese peroxidase (MnP) and laccase. In this work, the source of extracellular hydrogen peroxide required for MnP activity was investigated. Our attention was focused on the possibility that hydrogen peroxide might be generated by MnP itself through the oxidation of organic acids secreted by the fungus. Both oxalate and glyoxylate were found in the extracellular fluid ofC. subvermisporacultures grown in chemically defined media, where MnP is also secreted. The in vivo oxidation of oxalate was measured;14CO2evolution was monitored after addition of exogenous [14C]oxalate to cultures at constant specific activity. In standard cultures, evolution of CO2from oxalate was maximal at day 6, although the MnP titers were highest at day 12, the oxalate concentration was maximal (2.5 mM) at day 10, and the glyoxylate concentration was maximal (0.24 mM) at day 5. However, in cultures containing low nitrogen levels, in which the pH is more stable, a better correlation between MnP titers and mineralization of oxalate was observed. Both MnP activity and oxidation of [14C]oxalate were negligible in cultures lacking Mn(II). In vitro assays confirmed that Mn(II)-dependent oxidation of [14C]oxalate by MnP occurs and that this reaction is stimulated by glyoxylate at the concentrations found in cultures. In addition, both organic acids supported phenol red oxidation by MnP without added hydrogen peroxide, and glyoxylate was more reactive than oxalate in this reaction. Based on these results, a model is proposed for the extracellular production of hydrogen peroxide byC. subvermispora.
Effects of Temperature, Salinity, and Medium Composition on Compatible Solute Accumulation by
Thermococcus
spp
Authors: Lamosa Pedro , Martins Lígia O. , Da Costa Milton S. , Santos Helena
Published: December 2019

The effects of salinity and growth temperature on the accumulation of intracellular organic solutes were examined by nuclear magnetic resonance spectroscopy (NMR) in
Thermococcus litoralis
,
Thermococcus celer
,
Thermococcus stetteri
, and
Thermococcus zilligii
(strain AN1). In addition, the effects of growth stage and composition of the medium were studied in
T. litoralis
. A novel compound identified as β-galactopyranosyl-5-hydroxylysine was detected in
T. litoralis
grown on peptone-containing medium. Besides this newly discovered compound,
T. litoralis
accumulated mannosylglycerate, aspartate, α-glutamate, di-
myo
-inositol-1,1′(3,3′)-phosphate, hydroxyproline, and trehalose. The hydroxyproline and β-galactopyranosyl-5-hydroxylysine were probably derived from peptone, while the trehalose was derived from yeast extract; none of these three compounds was detected in the other
Thermococcus
strains examined. Di-
myo
-inositol-1,1′(3,3′)-phosphate, aspartate, and mannosylglycerate were detected in
T. celer
and
T. stetteri
, and the latter organism also accumulated α-glutamate. The only nonmarine species studied,
T. zilligii
, accumulated very low levels of α-glutamate and aspartate. The levels of mannosylglycerate and aspartate increased in
T. litoralis
,
T. celer
, and
T. stetteri
in response to salt stress, while di-
myo
-inositol-1,1′(3,3′)-phosphate was the major intracellular solute at supraoptimal growth temperatures. The phase of growth had a strong influence on the types and levels of compatible solutes in
T. litoralis
; mannosylglycerate and aspartate were the major solutes during exponential growth, while di-
myo
-inositol-1,1′(3,3′)-phosphate was the predominant organic solute during the stationary phase of growth. This work revealed an unexpected ability of
T. litoralis
to scavenge suitable components from the medium and to use them as compatible solutes.
Analysis of the Gene Cluster Encoding Toluene/
o
-Xylene Monooxygenase from
Pseudomonas stutzeri
OX1
Authors: Bertoni Giovanni , Martino Manuela , Galli Enrica , Barbieri Paola
Published: December 2019

The toluene/
o
-xylene monooxygenase cloned from
Pseudomonas stutzeri
OX1 displays a very broad range of substrates and a very peculiar regioselectivity, because it is able to hydroxylate more than one position on the aromatic ring of several hydrocarbons and phenols. The nucleotide sequence of the gene cluster coding for this enzymatic system has been determined. The sequence analysis revealed the presence of six open reading frames (ORFs) homologous to other genes clustered in operons coding for multicomponent monooxygenases found in benzene- and toluene-degradative pathways cloned from
Pseudomonas
strains. Significant similarities were also found with multicomponent monooxygenase systems for phenol, methane, alkene, and dimethyl sulfide cloned from different bacterial strains. The knockout of each ORF and complementation with the wild-type allele indicated that all six ORFs are essential for the full activity of the toluene/
o
-xylene monooxygenase in
Escherichia coli
. This analysis also shows that despite its activity on both hydrocarbons and phenols, toluene/
o
-xylene monooxygenase belongs to a toluene multicomponent monooxygenase subfamily rather than to the monooxygenases active on phenols.
Effect of Butyrolactone I on the Producing Fungus,
Aspergillus terreus
Authors: Schimmel Timothy G. , Coffman Allen D. , Parsons Sarah J.
Published: December 2019

Butyrolactone I [α-oxo-β-(
p
-hydroxyphenyl)-γ-(
p
-hydroxy-
m
-3,3-dimethylallyl-benzyl)-γ-methoxycarbonyl-γ-butyrolactone] is produced as a secondary metabolite by
Aspergillus terreus
. Because small butyrolactone-containing molecules act as self-regulating factors in some bacteria, the effects of butyrolactone I on the producing organism were studied; specifically, changes in morphology, sporulation, and secondary metabolism were studied. Threefold or greater increases in hyphal branching (with concomitant decreases in the average hyphal growth unit), submerged sporulation, and secondary metabolism were observed when butyrolactone I was added to cultures of
A. terreus
. Among the secondary metabolites whose production was increased by this treatment was the therapeutically important compound lovastatin. These findings indicate that butyrolactone I induces morphological and sporulation changes in
A. terreus
and enhances secondary metabolite production in a manner similar to that previously reported for filamentous bacteria.
Bias in Template-to-Product Ratios in Multitemplate PCR
Authors: Polz Martin F. , Cavanaugh Colleen M.
Published: December 2019

Bias introduced by the simultaneous amplification of specific genes from complex mixtures of templates remains poorly understood. To explore potential causes and the extent of bias in PCR amplification of 16S ribosomal DNAs (rDNAs), genomic DNAs of two closely and one distantly related bacterial species were mixed and amplified with universal, degenerate primers. Quantification and comparison of template and product ratios showed that there was considerable and reproducible overamplification of specific templates. Variability between replicates also contributed to the observed bias but in a comparatively minor way. Based on these initial observations, template dosage and differences in binding energies of permutations of the degenerate, universal primers were tested as two likely causes of this template-specific bias by using 16S rDNA templates modified by site-directed mutagenesis. When mixtures of mutagenized templates containing AT- and GC-rich priming sites were used, templates containing the GC-rich permutation amplified with higher efficiency, indicating that different primer binding energies may to a large extent be responsible for overamplification. In contrast, gene copy number was found to be an unlikely cause of the observed bias. Similarly, amplification from DNA extracted from a natural community to which different amounts of genomic DNA of a single bacterial species were added did not affect relative product ratios. Bias was reduced considerably by using high template concentrations, by performing fewer cycles, and by mixing replicate reaction preparations.
Biocatalyst Engineering by Assembly of Fatty Acid Transport and Oxidation Activities for In Vivo Application of Cytochrome P-450
BM-3
Monooxygenase
Authors: Schneider Silke , Wubbolts Marcel G. , Sanglard Dominique , Witholt Bernard
Published: December 2019

The application of whole cells containing cytochrome P-450
BM-3
monooxygenase [EC
1.14.14.1
] for the bioconversion of long-chain saturated fatty acids to ω-1, ω-2, and ω-3 hydroxy fatty acids was investigated. We utilized pentadecanoic acid and studied its conversion to a mixture of 12-, 13-, and 14-hydroxypentadecanoic acids by this monooxygenase. For this purpose,
Escherichia coli
recombinants containing plasmid pCYP102 producing the fatty acid monooxygenase cytochrome P-450
BM-3
were used. To overcome inefficient uptake of pentadecanoic acid by intact
E. coli
cells, we made use of a cloned fatty acid uptake system from
Pseudomonas oleovorans
which, in contrast to the common FadL fatty acid uptake system of
E. coli
, does not require coupling by FadD (acyl-coenzyme A synthetase) of the imported fatty acid to coenzyme A. This system from
P. oleovorans
is encoded by a gene carried by plasmid pGEc47, which has been shown to effect facilitated uptake of oleic acid in
E. coli
W3110 (M. Nieboer, Ph.D. thesis, University of Groningen, Groningen, The Netherlands, 1996). By using a double recombinant of
E. coli
K27, which is a
fadD
mutant and therefore unable to consume substrates or products via the β-oxidation cycle, a twofold increase in productivity was achieved. Applying cytochrome P-450
BM-3
monooxygenase as a biocatalyst in whole cells does not require the exogenous addition of the costly cofactor NADPH. In combination with the coenzyme A-independent fatty acid uptake system from
P. oleovorans
, cytochrome P-450
BM-3
recombinants appear to be useful alternatives to the enzymatic approach for the bioconversion of long-chain fatty acids to subterminal hydroxylated fatty acids.
Manganese Reduction by Microbes from Oxic Regions of the Lake Vanda (Antarctica) Water Column
Authors: Bratina Bonnie Jo , Stevenson Bradley S. , Green William J. , Schmidt Thomas M.
Published: December 2019

Depth profiles of metals in Lake Vanda, a permanently ice-covered, stratified Antarctic lake, suggest the importance of particulate manganese oxides in the scavenging, transport, and release of metals. Since manganese oxides can be solubilized by manganese-reducing bacteria, microbially mediated manganese reduction was investigated in Lake Vanda. Microbes concentrated from oxic regions of the water column, encompassing a peak of soluble manganese [Mn(II)], reduced synthetic manganese oxides (MnO
2
) when incubated aerobically. Pure cultures of manganese-reducing bacteria were readily isolated from waters collected near the oxic Mn(II) peak. Based on phylogenetic analysis of the 16S rRNA gene sequence, most of the isolated manganese reducers belong to the genus
Carnobacterium
. Cultures of a phylogenetically representative strain of
Carnobacterium
reduced synthetic MnO
2
in the presence of sodium azide, as was seen in field assays. Unlike anaerobes that utilize manganese oxides as terminal electron acceptors in respiration, isolates of the genus
Carnobacterium
reduced Mn(IV) via a diffusible compound under oxic conditions. The release of adsorbed trace metals accompanying the solubilization of manganese oxides may provide populations of
Carnobacterium
with a source of nutrients in this extremely oligotrophic environment.
Microbial Diversity in a Hydrocarbon- and Chlorinated-Solvent-Contaminated Aquifer Undergoing Intrinsic Bioremediation
Authors: Dojka Michael A. , Hugenholtz Philip , Haack Sheridan K. , Pace Norman R.
Published: December 2019

A culture-independent molecular phylogenetic approach was used to survey constituents of microbial communities associated with an aquifer contaminated with hydrocarbons (mainly jet fuel) and chlorinated solvents undergoing intrinsic bioremediation. Samples were obtained from three redox zones: methanogenic, methanogenic-sulfate reducing, and iron or sulfate reducing. Small-subunit rRNA genes were amplified directly from aquifer material DNA by PCR with universally conserved or
Bacteria
- or
Archaea
-specific primers and were cloned. A total of 812 clones were screened by restriction fragment length polymorphisms (RFLP), approximately 50% of which were unique. All RFLP types that occurred more than once in the libraries, as well as many of the unique types, were sequenced. A total of 104 (94 bacterial and 10 archaeal) sequence types were determined. Of the 94 bacterial sequence types, 10 have no phylogenetic association with known taxonomic divisions and are phylogenetically grouped in six novel division level groups (candidate divisions WS1 to WS6); 21 belong to four recently described candidate divisions with no cultivated representatives (OP5, OP8, OP10, and OP11); and 63 are phylogenetically associated with 10 well-recognized divisions. The physiology of two particularly abundant sequence types obtained from the methanogenic zone could be inferred from their phylogenetic association with groups of microorganisms with a consistent phenotype. One of these sequence types is associated with the genus
Syntrophus
;
Syntrophus
spp. produce energy from the anaerobic oxidation of organic acids, with the production of acetate and hydrogen. The organism represented by the other sequence type is closely related to
Methanosaeta
spp., which are known to be capable of energy generation only through aceticlastic methanogenesis. We hypothesize, therefore, that the terminal step of hydrocarbon degradation in the methanogenic zone of the aquifer is aceticlastic methanogenesis and that the microorganisms represented by these two sequence types occur in syntrophic association.