Miracle-dz/UniFAR-FTUs huggingface dataset:
Abundance and Structure Composition of nirK and nosZ Genes as Well as Denitrifying Activity in Heavy Metal-polluted Paddy Soils

ABSTRACT Denitrification is an important microbial process in soils and leads to the emission of nitrous oxide (N2O). However, studies about the microbial community involved in denitrification processes in polluted paddy fields are scarce. Here, we studied two rice paddies which had been polluted for more than three decades by metal mining and smelter activities. Abundance and community composition were determined using real-time polymerase chain reaction (PCR) assay and denaturing gradient gel electrophoresis of nitrite reductase and nitrous oxide reductase gene amplicons (nirK and nosZ), while denitrifying activities were assessed by measuring potential denitrifier enzyme activity. We found that the community structure of both nirK and nosZ containing denitrifiers shifted under pollution in the two rice paddies. All the retrieved nirK sequences did not group into either α- or β-proteobacteria, while most of the nosZ species were affiliated with α-proteobacteria. While the abundance of both nirK and nosZ was significantly reduced in the polluted soils at “Dexing” (with relatively higher Cu levels), these parameters did not change significantly at “Dabaoshan” (polluted with Cd, Pb, Cu, and Zn). Furthermore, total denitrifying activity and N2O production and reduction rates also only decreased under pollution at “Dexing. ” These findings suggest that nirK and nosZ containing denitrifier populations and their activities could be sensitive to considerable Cu pollution, which could potentially affect N2O release from polluted paddy soils.
Anaerobic lipopeptide biosurfactant production by an engineered bacterial strain for in situ microbial enhanced oil recovery

Bacillus mojavensis JF-2 produces water-soluble lipopeptide under aerobic conditions, while Pseudomonas stutzeri DQ1 grows rapidly under anaerobic conditions. These bacteria were used to construct an engineered strain for anaerobic lipopeptide production by protoplast fusion for potential use in microbially enhanced oil recovery (MEOR). The resulting fusant strain FA-2 produced lipopeptide (382 mg l−1) anaerobically at temperatures up to 50 °C, across a pH range of 4.5–10.0, and at salt concentrations as high as 10% NaCl. Experimental results from a physical simulation core at 39 °C suggest that FA-2 has potential for use in MEOR.
Master manipulation continued: feminizing Wolbachia endosymbiont distorts sex chromosome inheritance

32 Wolbachia is a maternally inherited ubiquitous endosymbiotic bacterium of 33 arthropods that displays a diverse repertoire of host reproductive manipulations. 34 For the first time, we demonstrate that Wolbachia manipulates sex chromosome 35 inheritance in a sexually reproducing insect. Eurema mandarina butterfly 36 females on Tanegashima Island, Japan, are infected with the wFem Wolbachia 37 strain and produce all-female offspring, while antibiotic treatment results in male 38 offspring. Fluorescence in situ hybridization (FISH) revealed that wFem-positive 39 and wFem-negative females have ZO and WZ sex chromosome sets, 40 respectively, demonstrating the predicted loss of the W chromosome from 41 wFem-infected lineages. Genomic quantitative polymerase chain reaction 42 (qPCR) analysis showed that wFem-positive females lay only ZO eggs that carry 43 a paternal Z, whereas females from lineages that are naturally wFem-negative 44 lay both WZ and ZZ eggs. In contrast, antibiotic treatment of adult wFem females 45 resulted in the production of ZO and ZZ eggs, suggesting that this Wolbachia 46 strain can induce meiotic drive. Moreover, most male offspring produced by 47 antibiotic-treated wFem females had a ZZ karyotype, implying reduced survival 48 of ZO individuals in the absence of feminizing effects of Wolbachia. Antibiotic 49 treatment of wFem-infected larvae induced male-specific splicing of the 50 doublesex (dsx) gene transcript, causing an intersex phenotype. Thus, the loss 51 of the female-determining W chromosome in ZO individuals is functionally 52 compensated by Wolbachia feminization. We discuss how Wolbachia may 53 manipulate oogenesis to cause meiotic drive and that Wolbachia may have 54 acquired this coordinated dual mode of reproductive manipulation first by the 55 evolution of feminization and then cytoplasmically induced meiotic drive. 56
Distinguishing distribution dynamics from temporary emigration using dynamic occupancy models

Dynamic occupancy models are popular for estimating dynamic distribution rates (colonization and extinction) from repeated presence/absence surveys of unmarked animals. This approach assumes closure among repeated samples within primary periods, allowing estimation of dynamic rates between these periods. However, the impact of temporary emigration (TE; reversible changes in sampling availability) on dynamic rate estimates has not been tested. Using simulated data, we investigated the degree to which TE could mislead researchers interested in quantifying dynamics. We then compared results from three avian point count datasets to evaluate the likelihood that TE confounds estimates of dynamics for 19 species under a popular sampling protocol. Simulated experiments indicated that when secondary periods were open to TE, presence of dynamics was correctly identified ≥95.1% of the time, and dynamic rate estimates were accurate. However, dynamic rate estimates were biased when secondary periods were closed to TE. In empirical datasets, dynamic occupancy models had greater support than closed models for all species when secondary sampling periods occurred in immediate succession (i.e. 3 samples within 10 min); however, our results suggest that this is because dynamic estimates were heavily influenced by TE. When counts within a primary period were separated by 24–48 hr, we found evidence of dynamics for less than half of these species. We recommend an alternative sampling approach that allows accurate estimation of dynamic rates when TE is of no interest, and introduce a novel model for estimating both processes simultaneously in rare cases where they are both of biological interest. Concern for violating the occupancy modelling closure assumption has led to widespread recommendations that samples within primary periods be conducted extremely close in time. However, this may not be the best approach when interest is in quantifying dynamic rates. While dynamic occupancy models provide estimates of “colonization” and “extinction,” these values do not inherently represent dynamics unless TE has been explicitly modelled or accounted for with sampling design. Naiveté to this fact can result in incorrect conclusions about biological processes.
Kakapo habitat selection on Hauturu-o-toi in relation to plant phenology

Kakapo (Strigops habroptilus) breed only when certain gymnosperm species produce unusually abundant mast seed crops, events that can occur up to 5 years apart. Kakapo were first translocated to the offshore island refuge of Hauturu-o-toi (Little Barrier Island) in 1982. Despite the absence of known breeding triggers, several breeding attempts did occur prior to the birds’ removal in 1999. Although kakapo were reintroduced to Hauturu in 2012, the question of what triggers them to breed there remains a mystery. This paper re-examines unanalysed datasets to explore the link between kakapo habitat selection and plant phenology patterns on Hauturu during the 1990s. By comparing plant phenology with breeding attempts, we provide insights into potential breeding triggers, and the potential future of Hauturu as a sustainable refuge. We also provide an account of plant phenology patterns occurring on Hauturu. Resource selection ratios were calculated to determine habitat selection preferences using kakapo location data and a vegetation map of Hauturu. Analysis of plant phenology within preferred habitats was then undertaken to determine potential breeding triggers using a dataset of over 70 plant species collected from 1991-1995. Female kakapo that attempted to breed on Hauturu preferred Agathis australis (kauri) dominated vegetation to any other vegetation type. Phenology patterns coincided with kakapo breeding attempts, and attempted breeding years on Hauturu were years with high A. australis female cone abundance. The association between A. australis and breeding suggests that A. australis cone production could trigger kakapo breeding on Hauturu. With an increasing kakapo population and a limited number of suitable refuges, understanding the potential reproductive productivity of kakapo on Hauturu will be vital for their future management and recovery.
Characterization of animal communities involved in seed dispersal and predation of Guibourtia tessmannii (Harms) J.Léonard, a species newly listed on Appendix II of CITES

TERRA Teaching and Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Li ege, Gembloux, Belgium Evolutionary Biology and Ecology Unit, CP 160/12, Facult e des Sciences, Universit e Libre de Bruxelles, Brussels, Belgium Nature+ asbl, Wavre, Belgium Analytical Chemistry, Department Agro-Bio Chemistry, Gembloux Agro-Bio Tech, University of Li ege, Gembloux, Belgium Centre for Research and Conservation, Royal Zoological Society of Antwerp (RZSA), Antwerp, Belgium Laboratoire de Physiologie Animale, Electrophysiologie et de Pharmacologie, Facult e des Sciences, Universit e des Sciences et Techniques de Masuku, Franceville, Gabon
Complementary, High-throughput Methods for Creating Multi-dimensional, PEG-based Biomaterials

Tunable biomaterials that mimic selected features of the extracellular matrix (ECM), such as its stiffness, protein composition, and dimensionality, are increasingly popular for studying how cells sense and respond to ECM cues. In the field, there exists a significant trade-off for how complex and how well these biomaterials represent the in vivo microenvironment, versus how easy they are to make and how adaptable they are to high-throughput fabrication techniques. To address this need to integrate more complex biomaterials design with high-throughput screening approaches, we present several methods to fabricate synthetic biomaterials in 96-well plates and demonstrate that they can be adapted to existing liquid handling robotics. These platforms include 1) glass bottom plates with covalently attached ECM proteins, and 2) hydrogels with tunable stiffness and protein composition with either cells seeded on the surface, or 3) laden within the three-dimensional hydrogel matrix. This study includes proof-of-concept results demonstrating control over breast cancer cell line phenotypes via these ECM cues in a high-throughput fashion. We foresee the use of these methods as a mechanism to bridge the gap between high-throughput cell-matrix screening and engineered ECM-mimicking biomaterials.
Nitrogenase and Hydrogenase of the Actinobacteria Frankia : From Gene Expression to Proteins Function

Frankia R43 is a filamentous actinobacteria, known for its ability to fix atmospheric nitrogen and to concomitantly produce hydrogen. Not much is understood about the variations in nitrogen fixation and hydrogen production among Frankia strains at the molecular level. Thus, studies providing direct comparisons between less known and well-annotated Frankia strains, may provide further information on the specific functions of the nitrogenase and hydrogenase(s). We compared candidate gene expression, protein sequence similarities and physiological activities of the well-annotated clade I Frankia casuarinae strain CcI3 and the recently sequenced lineage III Frankia strain R43. Our candidate genes, members of the nif gene cluster, involved in dinitrogen fixation, and genes encoding uptake hydrogenase (Hup) subunits, with an importance for energetic efficiency, were examined under varying oxygen and nitrogen conditions. Relative expression of almost all genes tested was higher in CcI3 than in R43, except nifK, following different but distinct expression patterns among all conditions. Candidate genes expression in CcI3 seemed more sensitive to oxygen than in R43, and the oxygen status seemed to influence gene expression much more than the nitrogen status per se.
Phytoplankton Species Composition, Abundance and Cell Size in San Francisco Bay: Microscopic Analyses of USGS Samples Collected 1992-2014

This Data Release makes available measurements of phytoplankton species composition, abundance and cell size made on samples collected in San Francisco Bay (CA) from April 1992 through March 2014. Phytoplankton samples were collected at 31 stations along a 145-km transect where the variability of salinity, temperature, turbidity and nutrient concentrations reflected a broad range of environmental factors that regulate phytoplankton growth and abundance (map of sampling locations is available on the project website at: https://sfbay.wr.usgs.gov/access/wqdata/overview/wherewhen/stnmap.html). Whole water samples were preserved with acid Lugol s solution, and 2 to 50 ml aliquots were settled in chambers for 6 to 24 hours (Utermohl 1958). Phytoplankton cells were then counted and identified using a phase-contrast inverted microscope at 125x magnification, all cells greater than 30 μm diameter were enumerated. Cells smaller than 30 μm were counted at 1250x magnification; following the APHA (1989) strip count method, at least 100 cells of the most numerous taxon were counted. Cell volumes were estimated from measured linear dimensions and geometric formulas that varied with cell shapes. Phytoplankton samples representing 923 distinct date, station and depths were included. The 16,442 entries in this dataset include 609 different taxa within 11 functional groups. Diatoms dominated the total biovolume contributed by each functional group (77%) followed by dinoflagellates (14%) and cryptophytes (4.5%). The top 5 species contributing to the summed biovolume in all samples were: Thalassiosira punctigera, Chaetoceros socialis, Ditylum brightwellii, Thalassiosira rotula and Noctiluca scintillans. By frequency of occurrence, the top 5 species were: Teleaulax amphioxeia, Nannochloropsis spp. , Plagioselmis prolonga var. nordica, Skeletonema costatum and Thalassiosira eccentrica. APHA. (1989). Standard methods for the examination of water and wastewater, 17th edn. American Public Health Association, Washington, DC Utermohl H. (1958). Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitt Int Verh Theor Angew Limnol 9:1-38
Identification of spinach SIAMESE and analysis of its function in plant immunity

Abstract Diseases cause a significant loss in both yield and quality of spinach. The cell cycle signalling pathway plays a central role in balancing development and immunity of plants. Cyclin-Dependent Kinase Inhibitor (CKI) is a core cell cycle regulator. It has been found that two Arabidopsis CKIs, SIAMESE (SIM) and SMR1 (SIAMESE-Related 1), function redundantly not only as negative regulators of cell proliferation but also as positive regulators of plant immunity. In the spinach genome, we identified a homologue of Arabidopsis SIM, referred to as Spinacia oleracea SIAMESE (SoSIM). To investigate the function of SoSIM, we introduced the 35S promoter-driven SoSIM (35S:SoSIM) into Arabidopsis sim smr1 double mutants. Over-expression of SoSIM phenocopied RNA interference of Cyclin-Dependent Kinase A1 (CDKA1) which exhibited dwarf and serrated leaves, confirming that SIM is a CDK inhibitor. Arabidopsis wild-type trichomes are single and unicellular, whereas sim smr1 mutant trichomes are clustered and multicellular. SoSIM restored wild-type trichome phenotype of sim smr1 mutant. The sim smr1 mutants were susceptible to the avirulent pathogen Pseudomonas syringae pv. maculicola as compared with wild-type plants. Our data showed that the resistance of 35S:SoSIM-transgenic sim smr1 lines to the pathogen was fully restored, indicating that SoSIM activates plant immunity. These data verify that SoSIM functions as its Arabidopsis counterpart in inhibition of plant development and activation of plant immunity. Therefore, SoSIM can be explored to control the balance between development and immunity in spinach.
Investigating the role of programmed necrosis in oncolytic adenovirus-induced death

Oncolytic viruses are a group of viruses that preferentially replicate in cancer cells and are a promising cancer treatment. However, how these oncolytic adenoviruses kill cancer cells is not fully understood. It was long thought that DNA viruses utilize apoptosis to induce cell death but there is now evidence that adenovirus and vaccinia cytotoxicity displays features of necrosis-like programmed cell death. In order to investigate the role of necrosis in cell death as a result of oncolytic adenovirus infection, a panel of ovarian cancer cells with varying sensitivities to the oncolytic adenoviral mutant dl922-947 was used. Cells infected with dl922- 947 displayed key features of necrotic death. Using necrosis inhibitors necrostatin-1, necrosulfonamide, GSK2791840B, GSK2399872B and GSK2393843A, as well as RNAi-mediated knockdown of RIPK1, RIPK3 or MLKL, I showed that cells undergo RIPK3-dependent necrosis and that blockage of the downstream effector mixed lineage kinase domain-like (MLKL) attenuated cell death. While Tumour necrosis factor-α (TNF-α)-induced programmed necrosis(Laster, Wood and Gooding 1988) relies on the (RHIM)-dependent interaction of RIPK1 and RIPK3 (Li et al. 2012, Wu et al. 2014), RIPK1 seems to be redundant for adenovirus-induced death. Further, the addition of TNF-α blocking antibody to virus-infected cells showed no effect on either cell death. Using a RIPK3 overexpression model, I showed that the amount adenovirus- induced cell death correlated with the amount of RIPK3 expression and that RIPK3 expression did not affect virus production, infectivity or the expression of viral proteins. Further, in vivo experiments using human xenografts showed that expression of RIPK3 significantly improved anti-tumour activity following intra-tumoural injection of dl922-947.
Four new species, DNA barcode library and pre-Pliocene speciation of the euedaphic Afromontane Clivinini genera Trilophidius and Antireicheia (Coleoptera: Carabidae, Scaritinae)

We describe and extensively illustrate four new species of euedaphic (= dwelling in the soil) Clivinini ground beetles: Trilophidius acastus sp. nov. and T. argus sp. nov. (both from Bioko, Equatorial Guinea), as well as Antireicheia calais sp. nov. and A. zetes sp. nov. (both from the South Pare Mountains, Tanzania). We generate and report all currently available DNA barcode (= cytochrome oxidase subunit I) data for euedaphic Afromontane Clivinini of the genera Trilophidius (2 species, four records) and Antireicheia (13 species, 43 records). We infer a phylogeny for these beetles using a Maximum Likelihood approach based upon a matrix of 53 sequenced specimens (dx.doi.org/10.5883/DS-ANTIREI) with 658 aligned positions. All nominative species represented by two or more sequences are recovered as monophyletic. Both new species of Trilophidius form a weakly supported clade, while all seven species of South African Antireicheia form a moderately supported clade. The genus Antireicheia and the geographical assemblage of its six Tanzanian species are not monophyletic. We perform divergence time estimation in Afrotropical Antireicheia , and our analysis indicates that these lineages diverged predominantly in the middle or late Miocene. We highlight the notable lack of phylogenetic hypothesis linked with the vaguely and variably defined taxon “subfamily Scaritinae” and its subordinated taxa.
In vitro flower induction and multiple shoot regeneration studies in Solanum americanum L. (solanaceae)

In vitro regeneration of Solanum americanum was achieved from explants like leaf and nodal Segments on MS medium with B5 vitamins supplemented with different concentrations and combinations of plant growth regulators. Multiple shoot induction was achieved from nodal explants cultured on MS medium supplemented with BAP 3.0 mg/L+2, 4-D 0.5 mg/L+GA3 2.0 mg/L. In vitro flower induction and multiple shoot induction was observed from leaf explants on MS medium combination with BAP 2.0 mg/L+2,4-D 1.0mg/L+IAA 1.0 mg/L. The regenerated shoots were transferred in to MS medium fortified with NAA, IBA and IAA for root induction. Soil, compost and sand (1:1:1) mixture was the most suitable planting substrate for hardening. Regenerated plants were successfully acclimatized and survived under ex vitro conditions.
Dynamical model of the CLC-2 ion channel exhibits a two-step gating mechanism

This work reports a Markov state model of the conformational dynamics involved in regulating the inner and outer gates of the CLC-2 ion channel. This dynamical model, based on 600 microseconds of molecular dynamics simulation, suggests a new mechanism for channel activation. Transition path analysis highlights a dominant pathway between a highly stable closed state (similar to known structures) and several new protein conformations not observed in any previously elucidated CLC structure. Movement from the closed state involves the intracellular rotation of the inner-gate backbone along residues S168-G169-I170. This rotated state is similar to that observed in the recent cryo-EM structure of the bovine CLC-K channel, but the volume of the intracellular (inner) region of the ion conduction pathway is expanded to a greater extent. From this state, which remains closed at the extracellular side, two additional states may be assumed, each involving a unique rotameric flip of the GLUex (E211) side chain. Both additional states involve conformational changes that orient GLUex away from the extracellular (outer) region of the ion conduction pathway. In the first additional state, the rotameric flip of GLUex results in an open, or near-open, channel pore. The equilibrium population of this state is low (~1%), consistent with the low open probability of CLC-2 in the absence of a membrane potential stimulus (0 mV). In the second additional state, GLUex rotates to occlude the channel pore. This state, which has a low equilibrium population (~1%), is only accessible when GLUex is protonated. Together, these pathways model the opening of both an inner and outer gate within the CLC-2 selectivity filter, as a function of GLUex protonation. Collectively, our findings build on and are consistent with known properties of CLC-2 and will guide future investigations into CLC-2 channel biophysics.
Drosophila PLP forms centriolar-clouds that promote centriole stability, cohesion and MT nucleation

Pericentrin is a conserved centrosomal protein whose dysfunction has been linked to several human diseases. The precise function of Pericentrin, however, is controversial. Here, we examine Drosophila Pericentrin-like- protein (PLP) function in vivo, in tissues that form both centrosomes and cilia. PLP mutant centrioles exhibit four major defects: (1) They are too short and have subtle structural defects; (2) They separate prematurely, and so overduplicate; (3) They organise fewer MTs during interphase; (4) They fail to establish and/or maintain a proper connection to the plasma membrane— although, surprisingly, mutant centrioles can still form an axoneme and recruit transition zone (TZ) proteins. We show that PLP helps to form “ pericentriolar clouds” of electron-dense material that emanate from the central cartwheel spokes and spread outward to surround the mother centriole. The partial loss of these structures may explain the complex centriole, centrosome and cilium defects we observe in PLP mutant cells.