bluuebunny/crossref_metadata_2025_split huggingface dataset:
The insertion of a mitochondrial selfish element into the nuclear genome and its consequences
Authors: Dutheil Julien Y. , Münch Karin , Schotanus Klaas , Stukenbrock Eva H. , Kahmann Regine 
Published: October 2019

AbstractHoming endonucleases (HE) are enzymes capable of cutting DNA at highly specific target sequences, the repair of the generated double-strand break resulting in the insertion of the HE-encoding gene (“homing” mechanism). HEs are present in all three domains of life and viruses; in eukaryotes, they are mostly found in the genomes of mitochondria and chloroplasts, as well as nuclear ribosomal RNAs. We here report the case of a HE that accidentally integrated into a telomeric region of the nuclear genome of the fungal maize pathogenUstilago maydis. We show that the gene has a mitochondrial origin, but its original copy is absent from theU. maydismitochondrial genome, suggesting a subsequent loss or a horizontal transfer from a different species. The telomeric HE underwent mutations in its active site and lost its original start codon. A potential other start codon was retained downstream, but we did not detect any significant transcription of the newly created open reading frame, suggesting that the inserted gene is not functional. Besides, the insertion site is located in a putative RecQ helicase gene, truncating the C-terminal domain of the protein. The truncated helicase is expressed during infection of the host, together with other homologous telomeric helicases. This unusual mutational event altered two genes: the integrated HE gene subsequently lost its homing activity, while its insertion created a truncated version of an existing gene, possibly altering its function. As the insertion is absent in other field isolates, suggesting that it is recent, theU. maydis521 reference strain offers a snapshot of this singular mutational event.
Developmental onset of enduring long-term potentiation in mouse hippocampus
Authors: Ostrovskaya Olga I. , Cao Guan , Eroglu Cagla , Harris Kristen M. 
Published: October 2019

ABSTRACTAnalysis of long-term potentiation (LTP) provides a powerful window into cellular mechanisms of learning and memory. Prior work shows late LTP (L-LTP), lasting >3 hours, occurs abruptly at postnatal day 12 (P12) in rat hippocampus. The goal here was to determine the developmental profile of synaptic plasticity leading to L-LTP in the mouse hippocampus. Two mouse strains and two mutations known to affect synaptic plasticity were chosen: C57BL/6 and Fmr1−/y on the C57BL/6 background, and 129SVE and Hevin−/− (Sparcl1−/−) on the 129SVE background. Like rats, hippocampal slices from all of the mice showed test pulse-induced depression early during development that was gradually resolved with maturation by 5 weeks. All the mouse strains showed a gradual progression between P10-P35 in the expression of short-term potentiation (STP), lasting ≤ one hour. In the 129SVE mice, L-LTP onset (>25% of slices) occurred by 3 weeks, reliable L-LTP (>50% slices) was achieved by 4 weeks, and Hevin−/− advanced this profile by one week. In the C57BL/6 mice, L-LTP onset occurred significantly later, over 3-4 weeks, and reliability was not achieved until 5 weeks. Although some of the Fmr1−/y mice showed L-LTP before 3 weeks, reliable L-LTP also was not achieved until 5 weeks. Two bouts of TBS separated by ≥90 minutes advanced the onset age of L-LTP in rats from P12 to P10. In contrast, L-LTP onset was not advanced in any of the mouse genotypes by multiple bouts of TBS at 90 or 180 minute intervals. These findings show important species differences in the onset of STP and L-LTP, which occur at the same age in rats but are sequentially acquired in mice.SIGNIFICANCE STATEMENTLong-term potentiation (LTP) is a cellular mechanism of learning and memory. Knowing the developmental profile for LTP provides a basis for investigating developmental abnormalities leading to intellectual disabilities and other neurodevelopmental disorders. Here we explore the developmental profile of LTP onset in two wild type mouse strains, C57BL/6 and 129SVE, together with Fmr1−/y and Hevin−/− (Sparcl1−/−) mutations that produce abnormalities in synaptic structure, plasticity, and development. Our data provide a foundation for future investigations into connections between structural and functional plasticity leading to developmental anomalies in the brain.
Assessing the specificity of the relationship between brain alpha oscillations and tonic pain
Authors: Valentini Elia , Halder Sebastian , McInnersey Daisy , Cooke Jason , Romei Vincenzo 
Published: October 2019

AbstractRecent research has pointed to alpha brain oscillations as a potential clinical biomarker for sensitivity to pain. In particular, researchers claimed that the slowing of individual alpha frequency (IAF) could be an objective marker of pain during prolonged nociceptive stimulation. However, prolonged pain has been also associated with increased IAF. To date, there is insufficient evidence to conclude that IAF can be a neural marker of pain.The current study aimed at elucidating the conflicting findings by assessing the specificity of the relationship between brain alpha oscillations and tonic pain. We recorded electroencephalography (EEG) on healthy volunteers during exposure to consecutive 5-minute sessions of painful hot water immersion, innocuous warm water immersion and an aversive, non-painful auditory stimulus, matched by unpleasantness to the painful condition. Participants rated stimulus unpleasantness throughout each condition. We also asked participants to sit still with eyes closed and eyes open right before and after the three experimental conditions in order to obtain a robust estimate of baseline alpha. Our findings revealed both increased and decreased IAF during tonic hot stimulation depending on the alpha range targeted (7-13 Hz vs. 8-10 Hz). In addition, they provide mild evidence for a negative relationship between IAF and the unpleasantness of the experience. Finally, we could not identify a difference between IAF during tonic hot temperature and during tonic auditory experience. Altogether, these findings emphasize a twofold frequency pattern (increase vs. decrease) for IAF during tonic thermal pain, thus indicating the need for robust methodological scrutiny of IAF as a neural marker of pain.
Genetic variation at 27 y-strs in four regions of bahrain
Authors: Al-Snan Noora R. , Messaoudi Safia A. , Khubrani Yahya M. , Wetton Jon H. , Jobling Mark A. , Bakhiet Moiz 
Published: October 2019

AbstractBahrain location in the Arabian Gulf contributed to the diversity of its indigenous population descended from Christian Arabs, Persians (Zoroastrians), Jews, and Aramaic-speaking agriculturalists. The aim of this study was to examine population substructure within Bahrain using the 27 Y-STRs (short tandem repeats) in the Yfiler Plus kit and to characterize the haplotypes of 562 unrelated Bahraini nationals, sub-divided into the four geographical regions - North, Capital, South and Muharraq. Yfiler Plus provided a significant improvement over the earlier 17-locus Yfiler kit in discrimination capacity, increasing it from 77% to 87.5%, but this value differed widely between regions from 98.4% in Muharraq to 75.2% in the Northern region, an unusually low value possibly as a consequence of the very rapid expansion in population size in the last 80 years. Clusters of closely related male lineages were seen, with only 79.4% of donors displaying unique haplotypes and 59% of instances of shared haplotypes occurring within, rather than between, regions. Haplogroup prediction indicated diverse origins of the population with a predominance of haplogroups J2 and J1, both typical of the Arabian Peninsula, but also haplogroups such as B2 and E1b1a originating in Africa and H, L and R2 indicative of migration from the east. Haplogroup frequencies differed significantly between regions with J2 significantly more common in the Northern region compared with the Southern possibly as a result of differential settlement with Baharna (descended from populations in which J2 predominates) and Arabs (both indigenous and migrant Huwala who are expected to have a higher frequency of J1). Our study illustrated the importance of encompassing geographical and social variation when constructing population databases and the need for highly discriminating multiplexes where rapid expansions have occurred within tightly bounded populations.
Size reductions and genomic changes associated with harvesting within two generations in wild walleye populations
Authors: Bowles Ella , Marin Kia , Mogensen Stephanie , Macleod Pamela , Fraser Dylan J. 
Published: October 2019

AbstractThe extent and rate of harvest-induced genetic changes in natural populations may impact population productivity, recovery and persistence. While there is substantial evidence for phenotypic changes in harvested fishes, knowledge of genetic change in the wild remains limited, as phenotypic and genetic data are seldom considered in tandem, and the number of generations needed for genetic changes to occur is not well understood. We quantified changes in size-at-age, sex-specific changes in body size, and genomic metrics in three harvested walleye (Sander vitreus) populations and a fourth reference population with low harvest levels over a 15-year period in Mistassini Lake, Quebec. We also collected Traditional Ecological Knowledge (TEK) surrounding concerns about these populations over time. Using ∼9000 SNPs, genomic metrics included changes in population structure, neutral genomic diversity, effective population size and signatures of selection. TEK revealed concerns about overall reductions in body size and number of fish caught. Smaller body size, smaller size-at-age, changing population structure (population differentiation within one river and homogenization between two others), and signatures of selection between historical and contemporary samples reflected coupled phenotypic and genomic change in the three harvested populations in both sexes, while no change occurred in the reference population. Sex-specific analyses revealed differences in both body size and genomic metrics but were inconclusive about whether one sex was disproportionately affected. Our results support that harvest-induced genetic changes can arise within 1-2.5 generations in long-lived wild fishes, demonstrating the need to investigate concerns about harvest-induced evolution quickly once they have been raised.
Organic management promotes natural pest control through enhanced plant resistance to insects
Authors: Blundell Robert , Schmidt Jennifer E. , Igwe Alexandria , Cheung Andrea L. , Vannette Rachel L. , Gaudin Amélie C.M. , Casteel Clare L. 
Published: October 2019

AbstractLower insect pest populations found on long-term organic farms have largely been attributed to increased biodiversity and abundance of beneficial predators. However, potential induction of plant defenses has largely been ignored. This study aims to determine whether host plant resistance mediates decreased pest populations in organic systems, and to identify the underpinning mechanisms. We demonstrate that greater numbers of leafhoppers (Circulifer tenellus) settle on tomatoes (Solanum lycopersicum) grown using conventional management as compared to organic. Soil microbiome sequencing, chemical analysis, and transgenic approaches, coupled with multi-model inference, suggest that changes in leafhopper settling between organically and conventionally-grown tomatoes are dependent on salicylic acid accumulation in the plant, likely mediated by rhizosphere microbial communities. These results suggest that organically-managed soils and microbial communities may play an unappreciated role in reducing plant attractiveness to pests by increasing plant resistance.
Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses
Authors: Shi Chengcheng , Han Kai , Li Liangwei , Seim Inge , Lee Simon Ming-Yuen , Xu Xun , Yang Huanming , Fan Guangyi , Liu Xin 
Published: October 2019

AbstractMangroves are main components of an ecosystem which connect land and ocean and is of significant ecological importance. They are found around the world and taxonomically distributed in 17 families. Until now there has been no evolutionary phylogenetic analyses on mangroves based on complete plastome sequences. In order to infer the relationship between mangroves and terrestrial plants at the molecular level, we generated chloroplast genomes of 14 mangrove species from eight families, spanning six orders: Fabales (Pongamia pinnata), Lamiales (Avicennia marina), Malpighiales (Excoecaria agallocha, Bruguiera sexangula, Kandelia obovata, Rhizophora stylosa, Ceriops tagal), Malvales (Hibiscus tiliaceus, Heritiera littoralis, Thespesia populnea), Myrtales (Laguncularia racemose, Sonneratia ovata, Pemphis acidula), and Sapindales (Xylocarpus moluccensis). The whole-genome length of these chloroplasts is from 149kb to 168kb. They have a conserved structure, with two Inverted Repeat (IRa and IRb, ~25.8kb), a large single-copy region (LSC, ~89.0kb), a short single-copy (SSC, ~18.9kb) region, as well as ~130 genes (85 protein-coding, 37 tRNA, and 8 rRNA). The number of simple sequence repeats (SSRs) varied between mangrove species. Phylogenetic analysis using complete chloroplast genomes of 71 mangrove and land plants, confirmed the previously reported phylogeny within rosids, including the positioning of obscure families such as Linaceae within Malpighiales. Most mangrove chloroplast genes are conserved and we found six genes subjected to positive or neutral selection. Genomic comparison showed IR regions have lower divergence than other regions. Our study firstly reported several plastid genetic resource for mangroves, and the determined evolutionary locations as well as comparative analyses of these species provid insights into the mangrove genetic and phylogenetic research.
Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies
Authors: Niemeyer Michael , Castillo Elena Moreno , Ihling Christian H. , Iacobucci Claudio , Wilde Verona , Hellmuth Antje , Hoehenwarter Wolfgang , Samodelov Sophia L. , Zurbriggen Matias D. , Kastritis Panagiotis L. , Sinz Andrea , Calderón Villalobos Luz Irina A. 
Published: October 2019

ABSTRACTCullin RING-type E3 ubiquitin ligases SCFTIR1/AFB1-5and their ubiquitylation targets, AUX/IAAs, sense auxin concentrations in the nucleus. TIR1 binds a surface-exposed degron in AUX/IAAs promoting their ubiquitylation and rapid auxin-regulated proteasomal degradation. Here, we resolved TIR1·auxin·IAA7 and TIR1·auxin·IAA12 complex topology, and show that flexible intrinsically disordered regions (IDRs) in the degron’s vicinity, cooperatively position AUX/IAAs on TIR1. The AUX/IAA PB1 interaction domain also assists in non-native contacts, affecting AUX/IAA dynamic interaction states. Our results establish a role for IDRs in modulating auxin receptor assemblies. By securing AUX/IAAs on two opposite surfaces of TIR1, IDR diversity supports locally tailored positioning for targeted ubiquitylation, and might provide conformational flexibility for adopting a multiplicity of functional states. We postulate IDRs in distinct members of the AUX/IAA family to be an adaptive signature for protein interaction and initiation region for proteasome recruitment.
Electron Microscopic Identification of Distant Metastatic Cell in Human Prostate Cancer in Tissue section
Authors: Sinha Akhouri A. 
Published: October 2019

AbstractMutation in chromatin/DNA/genes of stem cells is a prerequisite for the development of cancer in the benign prostate. Mutation imparts chronic proliferation advantage to invasive and metastatic cancer cells, but not in benign prostate. We hypothesize that identification of metastatic prostatic cancer (PC) cells in tissue sections can lead to an early diagnosis and treatment of patients, hopefully, reducing death due to this disease. We have tested our hypothesis using biopsy and/or radical prostatectomy specimens of untreated and DES (diethylstilbestrol)-treated prostate cancer and transmission electron microscopy. Materials and methods: Tissue samples embedded in Epon were thin sectioned and examined on RCA EMU 3 or 4 transmission electron microscope. Results: We have identified two types of PC stem cells. Invasive stem cell invades the adjacent stroma whereas metastatic cell, a lineage of stem cell, is dedifferentiated columnar/cuboidal cells. Metastatic cell is identified by nuclear plasticity (pleomorphic nucleus), loss of nuclear membranes, loss of boundary between nucleus and cytoplasm and presence of electron dense molecules. Nuclear chromatin/DNA appears as electron dense molecules which readily pass plasma and basement membranes and enter the capillary before adhering to the red cell surface. Electron dense molecules are found in capillary, undoubtedly, reach metastatic site (s). Discussion and conclusion: Chromatin/DNA are small molecules that can readily cross many barriers, unlike an individual cancer cell. We show that invasive a cell is stem cell and metastasis develops from dedifferentiated columnar/cuboidal nuclear electron dense molecules. This is the first study to cells characterize metastatic cell in tissue sections.
Evidence that stress-induced changes in surface temperature serve a thermoregulatory function
Authors: Robertson Joshua K. , Mastromonaco Gabriela , Burness Gary 
Published: October 2019

AbstractChanges in body temperature following exposure to stressors have been documented for nearly two millennia, however, the functional value of this phenomenon is poorly understood. We tested two competing hypotheses to explain stress-induced changes in temperature, with respect to surface tissues. Under the first hypothesis, changes in surface temperature are a consequence of vasoconstriction that occurs to attenuate blood-loss in the event of injury and serves no functional purposeper se;defined as the Haemoprotective Hypothesis. Under the second hypothesis, changes in surface temperature reduce thermoregulatory burdens experienced during activation of a stress response, and thus hold a direct functional value; here, the Thermoprotective Hypothesis. To understand whether stress-induced changes in surface temperature have functional consequences, we tested predictions of the Haemoprotective and Thermoprotective hypotheses by exposing Black-capped Chickadees (n = 20) to rotating stressors across an ecologically relevant ambient temperature gradient, while non-invasively monitoring surface temperature (eye region temperature) using infrared thermography. Our results show that individuals exposed to rotating stressors reduce surface temperature and dry heat loss at low ambient temperature and increase surface temperature and dry heat loss at high ambient temperature, when compared to controls. These results support the Thermoprotective Hypothesis and suggest that changes in surface temperature following stress exposure have functional consequences and are consistent with an adaptation. Such findings emphasize the importance of the thermal environment in shaping physiological responses to stressors in vertebrates, and in doing so, raise questions about their suitability within the context of a changing climate.Summary StatementWe provide empirical evidence for a functional value to stress-induced changes in surface temperature that is consistent with an adaptation, using a temperate endotherm (Black-capped Chickadee) as a model species.
Pervasively thinner neocortex as a transdiagnostic feature of general psychopathology
Authors: Romer Adrienne L. , Elliott Maxwell L. , Knodt Annchen R. , Sison Maria L. , Ireland David , Houts Renate , Ramrakha Sandhya , Poulton Richie , Keenan Ross , Melzer Tracy R. , Moffitt Terrie E. , Caspi Avshalom , Hariri Ahmad R. 
Published: October 2019

AbstractObjectiveNeuroimaging research has revealed that structural brain alterations are common across broad diagnostic families of disorders rather than specific to a single psychiatric disorder. Such overlap in the structural brain correlates of mental disorders mirrors already well-documented phenotypic comorbidity of psychiatric symptoms and diagnoses, which can be indexed by a general psychopathology orpfactor. We hypothesized that if general psychopathology drives the convergence of structural alterations common across disorders then 1) there should be few associations unique to any one diagnostic family of disorders, and 2) associations with thepfactor should overlap with those for the broader diagnostic families.MethodsAnalyses were conducted on structural MRI and psychopathology data collected from 861 members of the population representative Dunedin Study at age 45.ResultsStudy members with high scores across three broad diagnostic families of disorders (Externalizing, Internalizing, Thought Disorder) exhibited highly overlapping patterns of reduced global and widely distributed parcel-wise neocortical thickness. Study members with highpfactor scores exhibited patterns of reduced global and parcel-wise neocortical thickness nearly identical to those associated with the three broad diagnostic families.ConclusionsA pattern of pervasively reduced neocortical thickness appears common across all forms of mental disorders and may represent a transdiagnostic feature of general psychopathology. As has been documented with regard to symptoms and diagnoses, the underlying brain structural correlates of mental disorders may not exhibit specificity, the continued pursuit of which may limit progress toward more effective strategies for etiological understanding, prevention, and intervention.
Loss of NPC1 enhances phagocytic uptake and impairs lipid trafficking in microglia
Authors: Colombo Alessio , Dinkel Lina , Müller Stephan A. , Monasor Laura Sebastian , Schifferer Martina , Cantuti-Castelvetri Ludovico , König Jasmin , Vidatic Lea , Bremova-Ertl Tatiana , Hecimovic Silva , Simons Mikael , Lichtenthaler Stefan F. , Strupp Michael , Schneider Susanne A. , Tahirovic Sabina 
Published: October 2019

AbstractNiemann-Pick type C disease is a rare neurodegenerative disorder mainly caused by mutations inNpc1, resulting in abnormal late endosomal/lysosomal lipid storage. Although microgliosis is a prominent pathological feature, consequences of NPC1 loss on microglial function remain uncharacterized. Here, we provide an in-depth characterization of microglial proteomic signatures and phenotypes in a NPC1-deficient (Npc1-/-) murine model and patient blood-derived macrophages. We demonstrate enhanced phagocytic uptake and impaired lipid trafficking inNpc1-/-microglia that precede neuronal death. Loss of NPC1 compromises microglial developmental functions as revealed by increased synaptic pruning and deficient myelin turnover. Undigested myelin accumulates within multi-vesicular bodies ofNpc1-/-microglia while lysosomal degradation remains preserved. To translate our findings to human disease, we generated novelex vivoassays using patient macrophages that displayed similar proteomic disease signatures and lipid trafficking defects as murineNpc1-/-microglia. Thus, peripheral macrophages provide a novel promising clinical tool for monitoring disease progression and therapeutic efficacy in NPC patients. Our study underscores an essential role for NPC1 in immune cells and implies microglial therapeutic potential.