Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial Diversity in Linglong Gold Mine, China

ABSTRACT Bacteria have been actively regulating cycles of various elements in the environment. To explore the potential bacterial role in gold biogeochemical cycling, this study analyzed the bacterial diversity of mine rock (MR) and surface soil (SS) samples from Linglong gold mine using 16S rRNA gene clone library analysis and cultivation method. From MR, 24 operational taxonomic units (OTUs) were identified from MR, covering 3 phyla and 18 genera. Meanwhile, 24 OTUs were identified from SS, including 4 phyla and 18 genera. Compared with 16S rRNA gene clone library analysis, 28 aerobic and 34 anaerobic isolates were obtained, whereas 26 aerobic and 71 anaerobic strains were isolated from SS. The cultivable bacteria were affiliated with Firmicutes, Proteobacteria and Actinobacteria phyla, and dominated by Firmicutes. These results underscore the high level of bacterial diversity in the gold mine. Our study provides information on the microbial diversity in Linglong gold mine and sheds light on the existence and potential function of bacteria in the gold biogeochemical cycling.
Pre-processing of quantitative phenotypes from high throughput studies

High throughput phenotypic experiments include both deletion sets and R N A i experiments. They are genome wide and require much physical space. A s a result, multiple plates are often required in order to cover the whole genome. The use of multiple plates leads to systematic plate-wise experimental artefact, which impede statistical inference. In this paper, current pre-processing methodology wi l l be reviewed. Their fundamental principle is to align a common feature shared by al l plates. From this very principle, we propose an improved method which simultaneously estimates all parameters required for the pre-processing transformation. Some of the alignment features popular today implici t ly assume conditions which are often not met in practice. We discuss the various choices of features to align. Specifically, the upper quantiles and the mean of the left tai l trimmings of each plate's data distribution are features which are always available and simple to obtain. Moreover, they are robust to non-randomization of genes to plates. Their use wi l l be motivated through simulation and applied to real data. Applications to real data wi l l be used to demonstrate superiority over current methods as well as to discuss choices in transformation types.
A new species of Prismognathus Motschulsky from Xizang (Tibet), China (Coleoptera: Scarabaeoidea: Lucanidae)

A new species of stag beetle, Prismognathus prossi n. sp. , is described from Xizang (Tibet), China. The new species is compared with similar species, from which it differs in the peculiar shape of the eye canthus. The status of the type specimen of P. branczicki Nonfried is discussed. A checklist of the known species and subspecies of Prismognathus Motschulsky is also given.
Challenging the definition of the subfamily Usiinae: Phthiraxini, an unusual new tribe of bee flies (Diptera: Bombyliidae), based on Phthiraxia bowdeni gen. and sp. nov. from Western Australia

A new genus Phthiraxia gen. nov. (Usiinae: Phthiriini) is described from a remote region of Western Australia based on a male and a female specimen collected 35 years ago. The pair represent a single new species Phthiraxia bowdeni sp. nov. Two important characteristics of this new genus, however, challenge the definition of the subfamily Usiinae: the clypeus does not reach the base of antennae, and the palp is two‐segmented. Moreover, Phthiraxia gen. nov. has two other features: the wing vein M2 present, shared by all members of Phthiriini, and flagellum with subapical shallow sulcus containing a style, differentiating it from Phthiriini with a deep apical sulcus, and Usiini with a deep subapical sulcus. Results of a morphological phylogenetic analysis show that the new genus belongs to a lineage that is sister to the remaining members of the subfamily. Therefore, a monotypic new tribe, Phthiraxini tribus nov., is described to accommodate Phthiraxia gen. nov. A key to the Australian genera of Usiinae is provided. We reevaluate the syapomorphies of the Usiinae in light of the new tribe.
Effects of lines and inoculants on nutritive value and production costs of triticale silages

The current study was undertaken to investigate the ensilage characteristics in triticale lines treated by inoculants and their interaction on fermentation metabolites and rumen degradability. Costs were estimated for growing and feeding whole-crop triticale lines for animal production. Triticale hybrids were harvested at the dough stage of maturity (38% dry matter, DM). Plants were chopped approximately 2 cm after harvest and then treated with inoculants and were ensiled in 1.5-L mini laboratory silos. Two lactic acid bacterial inoculants with enzymes (LAB+enzymes I: Pediococcus acidilactici, Lactobacillus plantarum, and Streptococcus faecium with cellulase, hemicellulase, pentosanase, and amylase; LAB+enzyme II: P. acidilactici, L. plantarum, and amylase) were used as silage additives. Inoculants were applied at 1.5 × 105 cfu/g chopped fresh material. Silages with no additive served as the control. Four jars per treatment were sampled on day 60 after ensiling for chemical and microbiological analysis. At the end of the ensiling period (60 day), the silages were subjected to an aerobic stability test. The nutrient degradability of silages was determined in situ. Overall, there were no obvious interactions between triticale lines and the treatments for any of the parameters measured. The fermentation and nutritive value of silages were affected by treatments. LAB+enzymes increased the concentrations of lactic acid of the triticale silages and decreased the concentrations of butyric acid, total alcohols, and ammonia-N. Under aerobic conditions, LAB+enzyme treated silages had lower pH, CO2 production, and number of yeasts. Fibrous fractions were decreased with the application of LAB+enzymes. The 48 h in situ organic matter, DM, and neutral detergent fiber digestibility of the silages were enhanced by treatments. Addition LAB+enzymes to dough stage triticale silage reduces proteolysis; the inoculant possess antimicrobial properties and improves fermentation and nutritional value. The economic results are favorable financially for growing winter triticale as an animal feed in Mediterranean-type climates.
The Survival of Listeria monocytogenes on Fingertips and Factors Affecting Elimination of the Organism by Hand Washing and Disinfection.

The survival of Listeria monocytogenes applied to the fingertips was investigated using both an impression plate and an elution method. When suspended in saline, L. monocytogenes NCTC 9863 survived for up to 60 min on fingertips, but survival times were greatly extended when the inoculum was suspended in milk. Survival was not apparently affected by skin lipids, the skin's normal flora, or the fat content of the milk. Different serotypes displayed similar results for the percentage persistence over a 2-h period when suspended in milk except for an isolate of L. monocytogenes serotype 7 which had a greater percentage survival than other organisms tested. In contrast, Escherichia coli C600 failed to survive for one hour under the same conditions. Hand washing with either soap or a water-based chlorhexidine hand cleanser usually failed to decontaminate fingertips to which an inoculum of 104/CFU per fingertip suspended in milk was applied, but a solution of chlorhexidine gluconate in methanol was found to be effective.
Trophallactic transmission and metabolism of the active ingredient indoxacarb in Advion™ (Hymenoptera: Formicidae)

The new indoxacarb-based bait Advion™, which was developed for the control ofthe red imported fire ant (RIFA), Solenopsis invicta Buren, presumably capitalizes on the complex trophallaxis-driven social feeding behavior of the RIFA, as do other baits. It is believed that within the RIFA colony indoxacarb, which must first be metabolized by the insect in order to become acutely toxic, is metabolized by the larvae, though the ability of the other castes to metabolize indoxacarb remains unknown. The objective of this research was to demonstrate the trophallactic transmission of indoxacarb among RIFA, and to determine if RIFA workers can metabolize indoxacarb into the acutely toxic metabolite. In the laboratory, sets of 100 RIFA workers were painted, fed Calco blue-dyed Advion™ (which served as an indicator for the presence of indoxacarb) for 5 h, and then introduced into fluon-lined plastic shoe boxes containing either 1000 starved workers, or 1000 starved workers and ∼250 brood. After 24 h, select replicates were removed and all RIFA workers within were crushed. Results indicated that 50-55% (∼550-600) of the RIFA workers within each replicate contained Calco blue dye and, thus, indoxacarb, which demonstrated the trophallactic flow of indoxacarb among the RIFA. For the remaining replicates in which workers were not crushed, mortality was observed daily for 30 d. There was no significant difference (P>0.05) in mortality between replicates with workers only and replicates with both workers and brood, and both treatments resulted in ∼82% worker mortality by day 7, thus indicating that the workers were capable of metabolizing indoxacarb into the acutely toxic metabolite.
Manipulation of induced defenses in tomato by Colorado potato beetle: The effects of oral secretions and herbivore-associated microbes

Insect feeding consists of mechanical wounding and oral secretions (OS) which include saliva and/or regurgitant from digestive systems. When insect herbivores feed on plants, plants recognize herbivore-specific cues in OS and trigger biosynthesis of phytohormones such as jasmonic acid (JA) and salicylic acid (SA) and activate defense signaling pathways. Oral secretions play a critical role in mediating induced plant defenses. Here, I investigated the effects of OS from Colorado potato beetles (CPB) on the manipulation of induced defenses in tomato. First, I investigate the specificity of induced defenses in response to OS from lepidopteran species, tobacco hornworm (THW), and coleopteran species, CPB. I found that OS from CPB decreased defense gene transcripts compared with wounded control plants but OS from THW increased defense responses. This suggests that the specific response of induced defenses is attributed to OS from the herbivores. Next, I explored the underlying mechanisms of defense suppression by OS from CPB. Because herbivores possess microbial symbionts and herbivoreassociated microbes could change plant physiology, I investigated the effects of symbiotic microbes from CPB on plant defenses. I found that the symbiotic bacteria were secreted in OS during herbivory. By perceiving the beetle's attack as a microbial one, plants induced ineffective defense responses against CPB. The defense suppression was dependent on negative crosstalk between JA and SA signaling pathways. Finally, I investigated whether manipulation of induced defenses by the symbiotic bacteria from CPB occur in wild and cultivated Solanum plants. I found that antagonism between JA and SA was present in Solanum plants. In addition, the symbiotic bacteria suppressed defense responses in Solanum plants, suggesting that defense suppression by the symbiotic bacteria could help CPB adapt to host plants. This is the first study to demonstrate that herbivore-associated microbes manipulate plant defenses. This research will
In situ detection of transrenal gene mutations without DNA isolation and amplification using Array Piezoelectric Plate Sensor (PEPS)

In situ detection of transrenal gene mutations without DNA i solation and amplification using Array Piezoelectric Plate Sensor (PEPS). Ceyhun E. Kirimli Wan Y. Shih, Ph. D. Wei-Heng Shih, Ph. D. Low molecular weight (LMW) DNA fragments from distant organ s can pass through kidneys and exist in urine as ”transrenal DNA”. Transrenal D NA provides a noninvasive means to access cell-free DNAs from distant organs such as li ver, pancreas, colon that are otherwise difficult to obtain. Shih and Shih’s laboratory at Drexel has developed a highly sensitive piezoelectric plate sensor (PEPS) based on 8μm thick highly piezoelectric lead magnesium niobate-lead titanate (PMN-PT) freestanding la yer. For detection, receptor specific to a target analyte is immobilized on the PEPS. Bindi ng of the target analyte to the receptor on the PEPS surface decreases its resonance fre qu ncy. In-situ, label-free detection of the target analyte is achieved by monitoring th e PEPS resonance frequency shift. The detection resonance frequency shift of PEPS is en hanced more than 1000 times due to the PMN-PT layer’s capability to change its crystalli ne orientation upon analyte binding. As a result, PEPS has exhibited unprecedented atto molar (aM) sensitivity in labelfree detection of single-stranded DNA. The purpose of this study was to further develop PEPS as a tool for rapid (in< 40 min), label-free, multiplexed and highly sensitive detection of transrenal gene mutations of distant organs in urine. 1762T/1764A double mutation of hepati tis B virus (HBV), a risk factor associated with hepatocellular carcinoma (HCC) and Kras po int mutation at codon 12, a biomarker present in 50% of colorectal carcinomas (CRC) wil l be the model transrenal gene mutations in this study. To achieve the goal, a signal pr ocessing algorithm was devel-
Use of wild–caught individuals as a key factor for success in vertebrate translocations

La utilizacion de individuos capturados en el medio natural como factor fundamental del exito en las translocaciones de vertebrados Resulta fundamental que las translocaciones de vertebrados den buenos resultados para mejorar la eficacia y la eficiencia de las medidas de conservacion, si bien a menudo es dificil de evaluar debido a que los resultados negativos (translocaciones fallidas) raramente se publican. Elaboramos encuestas y las remitimos a los jefes de los servicios de conservacion de tres importantes regiones mediterraneas de Espana. La finalidad de nuestras encuestas era determinar el factor metodologico, que pudiera ponerse en practica con facilidad, mas influyente en el exito de las translocaciones. Entre estos factores figuraban la procedencia de los individuos translocados (cautividad o medio natural) y el esfuerzo de translocacion (tamano del propagulo y duracion del programa). Tras analizar 83 programas, correspondientes a 34 especies diferentes de vertebrados, por medio de modelos mixtos lineales generalizados, observamos que la procedencia era mas importante para el exito de la translocacion que el esfuerzo, si bien no pudimos descartar que este ultimo tuviera alguna influencia. La varianza en el exito de los programas de translocacion que utilizan individuos procedentes del medio natural fue inferior y, en consecuencia, los resultados, mas predecibles. La procedencia interacciono con los taxones de forma que el exito fue mayor cuando se utilizaron aves silvestres y, en especial, peces y mamiferos silvestres, pero no sucedio lo mismo cuando se liberaron reptiles. Por consiguiente, sugerimos que, para un esfuerzo dado, los resultados de la translocacion seran mejores para la mayoria de taxones de vertebrados si se utilizan individuos procedentes del medio natural. Cuando esto no sea posible, los gestores deberian liberar durante muchos anos individuos criados en cautividad.
Chemical and physical properties of an anthropogenic dark earth soil from Bragança, Para, Eastern Amazon

Although anthropogenic dark earth (ADE) is generally found in non-floodable land, it also occurs on floodplains but, there is no information about the chemical and physical characteristics of ADE in this environment. In this study, we propose to check the hypothesis that a Gleysol, classified as ADE, presents improved chemical and physical conditions than an adjacent soil, no anthropogenic. Thus, the objective of this study was to characterize the chemical and physical properties of the top layer of two ADE profiles in a Gleysol and compare them with an adjacent soil. Samples were taken from two areas classified as ADE in Braganca, Para State, Brazil, at the "Jabuti" archaeological site, and from an adjacent non-anthropogenic site. Disturbed and undisturbed soil samples were collected at the soil depth of 0.05-0.10 m for chemical (pH, potential acidity, exchangeable cations, and soil organic carbon) and physical (soil particle size distribution, particles density, water retention curve, total porosity, microporosity, macroporosity, and bulk density) analysis. The two areas of ADE in a Gleysol, showed improved soil chemical properties compared to the adjacent soil, particularly in relation to phosphorus and calcium levels that contributed to higher cation exchange capacity which, in turn, was positively related to organic carbon content. Changes in soil physical properties were less noticeable but both areas of ADE presented higher water retention capacity, particularly at low tension. The improved conditions of the ADE soil under Gleysols shows that these areas are adequate for soil cultivation, especially with plants adapted to floodplain.
Inhibition of Listeria in Buffer, Broth, and Milk by Enterocin 1146, a Bacteriocin Produced by Enterococcus faecium.

Enterocin 1146, a bacteriocin produced by Enterococcus faecium . DPC1146, has a rapid bactericidal effect on Listeria in buffer systems, broth, and milk. In trypticase soy broth, increasing the bacteriocin dose and/or decreasing the pH extended the lag phase of Listeria innocua . A logarithmic relationship was found between response (as proportion of survivors or growth compared to a control) and dose. Increasing the inoculum level of the indicator reduced the effectiveness of enterocin 1146. Log-phase cells of L. innocua were more resistant than stationary-phase cells in both broth and buffer systems. In milk treated with 250 arbitrary units of enterocin 1146/ml and inoculated with 103 or 105 CFU/ml of Listeria monocytogenes Scott A, populations reached only 5-14% of the control after 24 h at 30°C, with numbers exceeding 107, while at 6°C a slow decrease in population was found.
Evidence for a single panmictic and genetically diverse population of the coconut crab Birgus latro (Decapoda: Anomura: Coenobitidae) on Christmas Island in the Indian Ocean

For the coconut crab Birgus latro, Christmas Island in the Indian Ocean may be one of the last retreats where populations of this declining species are not threatened by overharvesting, as on many other mostly tropical Indo-Pacific islands within the species’ wide range. Nevertheless, the population on Christmas Island has experienced severe losses during the past decade owing to habitat destruction and road mortality. To assess the population’s evolutionary potential and identify the number of conservation units, we conducted a combined morphometric and population genetic analysis using microsatellite markers. The findings suggest that the population is genetically diverse and panmictic. Neither genetic nor morphometric analyses revealed any population substructuring. There was no genetic evidence for sex-biased dispersal. Single-sample estimators for the effective population size (Ne) ranged from 492 to infinity, with very wide confidence intervals; they should therefore be viewed with caution. It would be advisable to reanalyse Ne, preferably by temporal methods. Despite mixed results, there is stronger evidence against rather than for the occurrence of a recent genetic bottleneck. So far, the population of B. latro on Christmas Island may be considered as a single conservation management unit, this way simplifying future conservation efforts taken for this magnificent species.
Response Characteristics between Sulfate-Reducing Bacteria and Environmental Factors in Petroleum Hydrocarbon-Contaminated Field of Northeast China

ABSTRACT Lithology samples were collected from six sites of a petroleum hydrocarbon-contaminated site in northeast China along a contamination plume. The sulfate-reducing bacteria (SRB) diversity of all samples was analyzed by PCR-DGGE technology. The Shannon-Wiener indexes (1.004–3.665), Simpson indexes (0.516–0.907) and Pielou indexes (0.996–1.004) of all samples were used to characterize the abundances, advantages and evenness of the microbial communities. Additionally, Canoco for Windows 4.5 was utilized to analyze the correlation between dominant SRB and environmental factors. The results showed that the abundance, advantages and evenness of the sulfate-reducing bacterial community changed regularly along the contamination plume direction. The microbial homology of the samples was not high (0.25–0.80), and the dominant bacteria exhibited heteroplasmy. Additionally, the dominant bacteria were identified as uncultured bacteria. Canonical correspondence analysis (CCA) analysis showed that the distribution and structure of SRB communities were not obviously correlated with the concentration of total petroleum hydrocarbons (TPH), dissolved oxygen (DO) and other environmental factors. The results presented herein provide evidence of natural bioremediation in petroleum hydrocarbon-contaminated fields and information that will be useful to bioremediation of other contaminated fields.
Consensus movements by groups of sperm whales

When animals live in cohesive groups they need to make consensus decisions about movements. As a very large-scale example of communal movement, nomadic female sperm whales (Physeter macrocephalus) travel about 50 km per day as coherent groups of 10–50 animals spread over several km of ocean. From 543 h of data during which 3,873 headings of small clusters of whales or individual whales were recorded, I quantified the heading behavior of groups foraging off the Galapagos Islands. The groups made both sudden and gradual turns. Using piecewise regression models, I estimate that sudden and gradual turns in heading both occurred at rates of 0.10/h. The mean change in heading was 69° for sudden turns and 84° for gradual turns. The mean duration of gradual turns was 1.3 h, so turns were often slow. Using the recorded headings within 30 min of each of 1,798 focal headings, a regression of heading on time gave a mean rate of turn of the group and error of each focal heading about the mean heading. Absolute heading errors increased with absolute turn rate (rS = 0.241; P = 0.0000), so turns were often messy. Thus sperm whales often make slow and messy—likely democratic—consensus decisions when groups change heading.
GC-MS-Based Analysis of Chloroform Extracted Suberin-Associated Root Waxes from Arabidopsis and Other Plant Species

[Abstract] The periderm and exodermis of taproots and tuberous taproots contain an extracellular lipid polymer, suberin, deposited in their cell walls. This polymer is intractable in organic solvents, and is co-deposited with chloroform-extractable waxes. These suberin-associated root waxes are typically composed of alkanes, primary alcohols, fatty acids, alkyl ferulates, alkyl caffeates, and alkyl coumarates (Espelie et al., 1980; Li et al., 2007; Kosma et al., 2015). They are believed to contribute to the diffusion barrier properties of suberized cell walls (Soliday et al., 1979), and possibly have other roles yet to be discovered. Here we describe a protocol to extract and analyze waxes associated with root suberin. This fraction of aliphatic components is extracted by whole root immersion in chloroform, and is then chemically modified to prepare samples that are more suitable to gas-chromatography analysis. This protocol is optimized for Arabidopsis thaliana, but can be used with roots of other plants as described herein.