bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insect—symbiont gene expression in the midgut bacteriocytes of a blood-sucking parasite
Authors: Filip Husnik , Vaclav Hypsa , Alistair Darby 
Published: March 2019

AbstractBackgroundAnimals interact with a diverse array of both beneficial and detrimental microorganisms. These interactions sometimes spark obligate symbioses where the host depends on beneficial bacteria for survival and reproduction. In insects, these obligate symbioses in many cases allow feeding on nutritionally unbalanced diets such as plant sap and vertebrate blood. It is, however, still not clear how are these obligate intracellular symbioses maintained at the cellular level for up to several hundred million years. Exact mechanisms driving host-symbiont interactions are only understood for a handful of model species and data on blood-feeding hosts with intracellular bacteria are particularly scarce.ResultsHere, we analyzed interactions at the symbiotic interfaces of an obligately blood-sucking parasite of sheep, the louse flyMelophagus ovinus. We assembled a reference transcriptome from one male and one female individual and used RNA-Seq with five biological replicates to compare expression in the midgut cells housing bacteria to the rest of the gut (foregut-hindgut). We focused on nutritional and immunity interactions between the insect host and its obligate symbiontArsenophonus melophagi, and also generated lower-coverage data for three facultative bacterial symbionts (Sodalis melophagi, Bartonella melophagi, andWolbachiasp.) and one facultative eukaryoteTrypanosoma melophagium. We found strong evidence for the importance of zinc in the system likely caused by symbionts using zinc-dependent proteases when acquiring amino acids, and for likely different immunity mechanisms controlling the symbionts than in closely related tsetse flies.ConclusionsOur results show that cellular and nutritional interactions between this blood-sucking insect and its symbionts are less intimate than what was previously found in some (but not all) plant-sap sucking insects such as aphids, psyllids, whiteflies, and mealybugs. This finding is likely interconnected to several features observed in symbionts in blood-sucking arthropods, particularly their midgut intracellular localization (as opposed to being localized in truly specialized bacteriocytes), intracytoplasmic presence (as opposed to having an outermost host-derived ‘symbiosomal’ membrane), less severe genome reduction, and relatively recent associations caused by frequent evolutionary losses and replacements.Data depositionRaw RNA-Seq data were made available through the European Nucleotide Archive (ENA) database under the study accession number PRJEB30632. All assemblies and additional large supplementary files are available on FigShare [https://doi.org/10.6084/m9.figshare.6146777.v1]. All commands used for data analyses are available on Github [https://github.com/filip-husnik/melophagus].
The orientation of a membrane probe from structural analysis by enhanced Raman scattering
Authors: Hughes Hannah J. , Demers Steven M. E. , Zhang Aobo , Hafner Jason H. 
Published: March 2019

ABSTRACTSmall fluorescent molecules are widely used as probes of biomembranes. Different probes optically indicate membrane properties such as the lipid phase, thickness, viscosity, and electrical potential. The detailed molecular mechanisms behind probe signals are not well understood, in part due to the lack of tools to determine probe position and orientation in the membrane. Optical measurements on aligned biomembranes and lipid bilayers provide some degree of orientational information based on anisotropy in absorption, fluorescence, or nonlinear optical properties. These methods typically find the polar tilt angle between the membrane normal and the long axis of the molecule. Here we show that solution-phase surface enhanced Raman scattering (SERS) spectra of lipid membranes on gold nanorods can be used to determine molecular orientation of molecules within the membrane. The voltage sensitive dye 4-(2-(6-(dibutylamino)-2-naphthalenyl)ethenyl)-1-(3-sulfopropyl)-hydroxide, known as di-4-ANEPPS, is studied. Through the analysis of several peaks in the SERS spectrum, the polar angle from the membrane normal is found to be 63°, and the roll angle around the long axis of the molecule to be 305° from the original orientation. This structural analysis method could help elucidate the meaning of fluorescent membrane probe signals, and how they are affected by different lipid compositions.
COMMD1 and PtdIns(4,5)P2 interaction maintain ATP7B copper transporter trafficking fidelity in HepG2 cells
Authors: Stewart Davis J. , Short Kristopher K. , Maniaci Breanna N. , Burkhead Jason L. 
Published: March 2019

ABSTRACTCopper-responsive intracellular ATP7B trafficking is critical to maintain copper balance in mammalian hepatocytes and thus organismal copper levels. The COMMD1 protein binds both the ATP7B copper transporter and phosphatidylinositol (4,5)-bisphosphate (PtdIns(4,5)P2), while COMMD1 loss causes hepatocyte copper accumulation. Although it is clear that COMMD1 is included in endocytic trafficking complexes, a direct function for COMMD1 in ATP7B trafficking has not been defined. In this study, experiments using quantitative reveal that COMMD1 modulates the copper-responsive ATP7B trafficking through recruitment to PtdIns(4,5)P2. Decreased COMMD1 abundance results in loss of ATP7B from lysosomes and thetrans-Golgi network (TGN) in high copper conditions, while excess expression of COMMD1 also disrupts ATP7B trafficking and TGN structure. Overexpression of COMMD1 mutated to inhibit PtdIns(4,5)P2binding has little impact on ATP7B trafficking. A mechanistic PtdIns(4,5)P2-mediated function for COMMD1 is proposed that is consistent with decreased cellular copper export due to disruption of the ATP7B trafficking itinerary and accumulation in the early endosome when COMMD1 is depleted. PtdIns(4,5)P2interaction with COMMD1 as well as COMMD1 abundance may both be important in maintenance of specific membrane protein trafficking pathways.SUMMARYQuantitative analysis of 3D protein colocalization defines the cellular function of COMMD1 in maintenance of ATP7B copper transporter trafficking fidelity and the importance of PtdIns(4,5)P2in this action.
Associations among Fish Length, Dam Passage History, and Survival to Adulthood in Two At-Risk Species of Pacific Salmon
Authors: Faulkner James R. , Bellerud Blane L. , Widener Daniel L. , Zabel Richard W. 
Published: March 2019

AbstractThreatened or endangered salmon and steelhead originating in the Snake River basin must pass through a series of eight major hydroelectric dams during their seaward migration. Understanding the effects of specific dam passage routes on lifetime survival for these stocks is essential for successful management. Juvenile fish may pass these dams via three primary routes: 1) spillways; 2) turbines; or 3) juvenile bypass systems, which divert fish away from turbines and route them downstream. Bypass systems may expose fish to trauma, increased stress, or disease. However, numerous studies have indicated that direct survival through bypass systems is comparable to and often higher than that through spillways. Some researchers have suggested that route of dam passage affects mortality in the estuary or ocean, but this is complicated by studies finding fish size affects route of passage. We tested whether passage through bypass systems was associated with probability of adult return after accounting for fish length and other covariates for two species of concern. We also investigated the association between fish length and probability of bypass at dams, and how this relationship could lead to spurious conclusions regarding effects of bypass systems on survival if length was ignored. We found that: 1) larger fish had lower bypass probabilities at 6 of 7 dams; 2) larger fish had higher probability of surviving to adulthood; 3) bypass history had little association with adult return after accounting for length; and 4) simulations indicated spurious effects of bypass on survival may arise when no true bypass effect exists, especially in models without length. Our results suggest that after fish leave the hydropower system, bypass passage history has little effect on mortality. Our findings underscore the importance of accounting for fish size in studies of dam passage or survival.
In search of Universal Cortical Power Changes Linked to NMDA-Antagonist based Anesthetic Induced Reductions in Consciousness
Authors: Pelentritou Andria , Kuhlmann Levin , Cormack John , Mcguigan Steven , Woods Will , Muthukumaraswamy Suresh , Liley David 
Published: March 2019

B. AbstractBackground.Despite their intriguing nature, investigations of the neurophysiology of N-methyl-D-aspartate (NMDA)-antagonists Xenon (Xe) and nitrous oxide (N2O) are limited and have revealed inconsistent frequency-dependent alterations, in spectral power and functional connectivity. Discrepancies are likely due to using low resolution electroencephalography restricted to sensor level changes, concomitant anesthetic agent administration and dosage. Our intention was to describe the effects of equivalent stepwise levels of Xe and N2O administration on oscillatory source power using a crossover design, to explore universal mechanisms of NMDA-based anesthesia.Methods.22 healthy males participated in a study of simultaneous magnetoencephalography and electroencephalography recordings. In separate sessions, equivalent subanesthetic doses of gaseous anesthetic agents N2O and Xe (0.25, 0.50, 0.75 equi MAC-awake) and 1.30 MAC-awake Xe (for Loss of Responsiveness) were administered. Source power in various frequency bands was computed and statistically assessed relative to a conscious baseline.Results.Delta (l-4Hz) and theta (4-8Hz) band power was significantly increased at the highest Xe concentration (42%, 1.30 MAC-awake) relative to baseline for both magnetoencephalography and electroencephalography source power (p<0.005). A reduction in frontal alpha (8-13 Hz) power was observed upon N2O administration, and shown to be stronger than equivalent Xe dosage reductions (p=0.005). Higher frequency activity increases were observed in magnetoencephalographic but not encephalographic signals for N2O alone with occipital low gamma (30-49Hz) and widespread high gamma (51-99Hz) rise in source power.Conclusions.Magnetoencephalography source imaging revealed unequivocal and widespread power changes in dissociative anesthesia, which were divergent to source electroencephalography. Loss of Responsiveness anesthesia at 42% Xe (1.30 MAC-awake) demonstrated, similar to inductive agents, low frequency power increases in frontal delta and global theta. N2O sedation yielded a rise in high frequency power in the gamma range which was primarily occipital for lower gamma bandwidth (3049 Hz) and substantially decreased alpha power, particularly in frontal regions.Clinical trial number and Registry URLNot applicable.Prior PresentationsPelentritou Andria, Kuhlmann Levin; Lee Heonsoo; Cormack John; Mcguigan Steven; Woods Will; Sleigh Jamie; Lee UnCheol; Muthukumaraswamy Suresh; Liley David. Searching For Universal Cortical Power Changes Linked To Anesthetic Induced Reductions In Consciousness. The Science of Consciousness April 4th2018. Tucson, Arizona, USA.Summary StatementNot applicable.
The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data
Authors: Torrenté Laurence de , Zimmerman Samuel , Suzuki Masako , Christopeit Maximilian , Greally John M. , Mar Jessica C. 
Published: March 2019

AbstractIn genomics, we often impose the assumption that gene expression data follows a specific distribution. However, rarely do we stop to question this assumption or consider its applicability to all genes in the transcriptome. Our study investigated the prevalence of genes with expression distributions that are non-Normal in three different tumor types from the Cancer Genome Atlas (TCGA). Surprisingly, less than 50% of all genes were Normally-distributed, with other distributions including Gamma, Bimodal, Cauchy, and Lognormal were represented. Relevant information about cancer biology was captured by the genes with non-Normal gene expression. When used for classification, the set of non-Normal genes were able to discriminate between cancer patients with poor versus good survival status. Our results highlight the value of studying a gene’s distribution shape to model heterogeneity of transcriptomic data. These insights would have been overlooked when using standard approaches that assume all genes follow the same type of distribution in a patient cohort.
Serum antibody profiles in individuals with latent Mycobacterium tuberculosis infection
Authors: Maekura Ryoji , Kitada Seigo , Osada‐Oka Mayuko , Tateishi Yoshitaka , Ozeki Yuriko , Fujicawa Takeya , Miki Mari , Jyunnko Ogawa , Mori Masahide , Matsumoto Sohkichi 
Published: March 2019

AbstractOne‐third of the world's humans has latent tuberculosis infection (LTBI), representing a large pool of potentially active TB. Recent LTBI carries a higher risk of disease progression than remote LTBI. Recent studies suggest important roles of antibodies in TB pathology, prompting us to investigate serum antibody profiles in a cohort with LTBI. In this single‐center prospective observational study, we analyzed IgG‐antibody concentrations against five major Mycobacterium tuberculosis (Mtb) antigens (including 6 kDa early secretory antigenic target (ESAT6), CFP10, and antigen 85A, which are expressed mainly in the growth phase; and mycobacterial DNA‐binding protein 1 (MDP1) and alpha‐crystallin like protein (Acr), which are expressed in the dormant phases) in individuals with recent (n=13) or remote (n=12) LTBI, no Mtb infection (n=19), or active TB (n=15). Antibody titers against ESAT6 and MDP1 were significantly higher in individuals with recent LTBI than in those with no Mtb infection or remote LTBI. All pairwise antibody titers against these five major antigens were significantly correlated throughout the stages of Mtb infection. Five individuals with recent LTBI had significantly higher antibody titers against ESAT6 (P = 0.03), Ag85A (P = 0.048), Acr (P = 0.057), and MDP1 (P = 0.0001) than in individuals with remote LTBI; they were also outside the normal range (+2 SDs). One of these individuals was diagnosed with active pulmonary TB at 18‐month follow‐up examination. These findings indicated that concentrations of antibodies against both multiplying and dormant Mtb are higher in recent LTBI and that individuals with markedly higher antibody titers may be appropriate candidates for prophylactic therapy.
Association of interleukin‐17 gene polymorphisms and susceptibility to brucellosis in Hamadan, western Iran
Authors: Keramat Fariba , Kazemi Sima , Saidijam Massoud , Zamani Alireza , Kohan Hamed Farhdi , Mamani Mojgan , Eini Peyman , Moghimbigi Abbas , Alikhani Mohammad Yousef 
Published: March 2019

AbstractIL‐17is one of the most important inflammatory cytokines that stimulate immunity responses in humans infected with Brucella species, acting as a regulator that reduces release of γ‐IFN, thus increasing resistance to brucellosis. Gene polymorphisms in the regulatory regions of cytokine‐encoding genes affect the amountsof cytokines produced and play a fundamental role in infectious diseases. The aim of this study was to determine the association between IL‐17 gene polymorphisms and susceptibility to brucellosis. In this case‐control study, 86 patients with brucellosis and 86 healthy persons in Hamadan, western Iran, from September 2014 to September 2016, were included. IL‐17 genetic variants at positions rs4711998 A/G, rs8193036 C/T, rs3819024 A/G, rs2275913 A/G, rs3819025 A/G, rs8193038 A/G, rs3804513 A/T, rs1974226 A/G and rs3748067 A/G were analyzed by restriction fragment length polymorphism‐PCR. Serum IL‐17 titers were measured by sandwich ELISA. GG genotypes at positions rs4711998 and rs3748067 were present significantly more frequently in patients with brucellosis than in controls (P < 0.05). The AA genotype at positions rs4711998, rs2275913 and rs3748067 and GG genotype at position rs19744226 were present significantly more frequently in controls than in the patient group. These results suggest that the AA genotype at positions rs3748067, rs3819025 and rs4711998 and GG genotype at position rs3819024 are likely protective factors against brucellosis, whereas the GG genotype at positions rs3748067, rs3819025 and rs4711998 and AA genotype at position rs3819024 may be risk factors against the disease. No significant relationships were found between serum IL‐17 titers and genotypes of the single‐nucleotide polymorphisms.
Insect acoustic communication: The role of transmission channel and the sensory system and brain of receivers
Authors: Römer Heiner 
Published: March 2019

Abstract

For decades, acoustic insects have been used as model organisms for behavioural neurobiologists to understand mate choice or predator avoidance, because behaviour can easily and reliably be elicited in the laboratory, and behaviourally relevant, identified nerve cells be studied under these conditions. However, signalling often takes place in complex environments, in which the signal perceived by the receiver may differ greatly from the one broadcast due to the biotic and abiotic properties of the sound transmission channel. Thus, the key challenge is to transfer the insights of these laboratory‐oriented experiments to more natural settings.

Signal detection, identification and discrimination, as well as localization, are complicated by the transmission channel in several ways. Here, I review the empirical evidence from outdoor studies, demonstrating how excess attenuation reduces the active space and the information of a signal at some distance from the sender. At the same time, these frequency‐dependent processes allow to maintain acoustic distances to neighbours in a population.

Insects often communicate within choruses of signallers of the same and different species, giving rise to high levels of acoustic masking interference. I discuss the evidence found for temporal or spatial partitioning of species in multispecies assemblages, and I show that solutions to the masking problem are based on a combination of adaptations in the behaviour of signallers and in the sensory system of receivers.

Whether or not the perceived signal elicits a behaviour in receivers will depend on the design of the sensory system and the brain. I give examples for active mechanical processes in insect sensory receptors that influence the responses to external stimuli. In addition, neuronal filters in the frequency, intensity or time domain, and even the memory of individual receivers, provide the basis for adaptive receiver decision‐making in mate choice scenarios.

Finally, I describe the advantages of having access to the relatively simple nervous systems of insects and how this access, combined with the use of a variety of behavioural tests, allows new insights into acoustic communication and its evolution.

A free Plain Language Summary can be found within the Supporting Information of this article.
Patchy delivery of functions undermines functional redundancy in a high diversity system
Authors: Streit Robert P. , Cumming Graeme S. , Bellwood David R. 
Published: March 2019

Abstract

Globally, many ecosystems are being challenged and transformed by anthropogenic climate change. Future ecosystem configurations will be heavily influenced by the critical ecological functions that affect resilience. Robust measures of these functions will thus be essential for understanding and responding to ecological change.

Coral reefs are experiencing unprecedented ecological change due to global mass coral bleaching. After bleaching events and other disturbances, herbivorous fishes provide functions that are critical for reef resilience by controlling harmful proliferation of algae. Identifying functional diversity amongst herbivorous fishes has been a mainstay of reef fish research, but it has remained unclear how, and to what extent, functional diversity translates to functional impacts on reefs.

Rather than assessing the functional potential of the herbivorous fish community, we explicitly considered the delivery of herbivory to the reef by quantifying, in unprecedented detail, the spatial extent and overlap of feeding areas across different functional groups. Core feeding areas were highly concentrated and consistently covered just 14% of available reef space. Overlap across functional groups was limited, showing high spatial complementarity as functional groups tended to feed next to one another. Thus, the delivery of critical ecosystem processes was patchy, effectively reducing functional redundancy, even in the presence of a diverse fish assemblage.

Our findings caution against assumptions of spatial homogeneity in the delivery of critical ecosystem functions. The functional impact of local herbivorous fish assemblages in current approaches may be overestimated, potentially leading to skewed assessments of reef resilience. Our results highlight the need to incorporate collective animal behaviour and spatio‐temporal scales into future assessments of ecosystem functions and ultimately ecological resilience.

A plain language summary is available for this article.
Specialized roots of Velloziaceae weather quartzite rock while mobilizing phosphorus using carboxylates
Authors: Teodoro Grazielle Sales , Lambers Hans , Nascimento Diego L. , de Britto Costa Patrícia , Flores‐Borges Denisele N. A. , Abrahão Anna , Mayer Juliana L. S. , Sawaya Alexandra C. H. F. , Ladeira Francisco Sérgio Bernardes , Abdala Dalton Belchior , Pérez Carlos A. , Oliveira Rafael S. 
Published: March 2019

Abstract

Campos rupestres is an extremely phosphorus (P)‐impoverished rocky ecosystem in Brazil. Velloziaceae is an important plant family in this environment, and some species colonize exposed quartzite rock. However, we know virtually nothing about their root development and nutrient acquisition within the rock outcrops and their possible role in rock weathering and landscape formation.

We tested the hypothesis that Velloziaceae dissolve P from the rock, enhancing rock weathering. The study was carried out with two Barbacenia species (Velloziaceae) that colonize quartzite rocks. We assessed the root specializations and exudates, and determined the mineralogical composition of the rocks.

The quartzite rocks contained a low concentration of total P in a matrix composed predominantly of silica. Using transmission electron microscopy, we show root growth perpendicular to the rock‐bedding planes. A micro‐XRF set‐up at the XRF beamline of a synchrotron evidenced root‐associated rock dissolution.

The investigated roots show novel morphological and physiological specializations, coined vellozioid roots, which are highly effective at P acquisition. These carboxylate‐releasing roots function like other specialized roots in nutrient‐depleted soils. The rocks represent a barrier for most species, but due to their chemical and physical actions inside the rocks, vellozioid roots play a pivotal role in rock weathering, contributing to shaping the campos rupestres landscapes.

A plain language summary is available for this article.