Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrogen addition and ecosystem functioning: Both species abundances and traits alter community structure and function

Increased nutrient inputs can cause shifts in plant community composition and plant functional traits, both of which affect ecosystem function. We studied community- and species-level leaf functional trait changes in a full factorial nitrogen (N), phosphorus (P), and potassium (K) fertilization experiment in a semi-arid grassland. Nitrogen was the only nutrient addition to signi ﬁ cantly affect leaf functional traits, and N addition increased community-weighted speci ﬁ c leaf area (SLA) by 19%, leaf chlorophyll content by 34%, height by 26%, and leaf dry matter content (LDMC) decreased by 11% while leaf thickness and toughness did not change signi ﬁ cantly. At the species level, most species contributed to the community-weighted trait and increased in SLA, chlorophyll, height, and LDMC with N addition. These intraspeci ﬁ c changes in functional traits account for 51 – 71% of the community-level changes in SLA, chlorophyll, plant height, and LDMC. The remaining change is due to species abundance changes; the two most abundant species ( Bouteloua gracilis and Carex ﬁ lifolia ) decreased in abundance with N addition while subdominant species increased in abundance. We also found annual variation in SLA, chlorophyll, plant height, and LDMC to be as important in in ﬂ uencing traits as N addition, likely due to differences in precipitation. Aboveground net primary productivity (ANPP) did not change signi ﬁ cantly with N addition. However, N addition caused a 34% increase in leaf area index (LAI) and a 67% increase in canopy chlorophyll density. We demonstrate that nitrogen-induced changes in both functional traits and species abundances magnify ANPP changes in LAI and canopy chlorophyll density. Therefore, ANPP underestimates N addition-induced ecosystem-level changes in the canopy vegetation.
Prevalence, Screening and Characterization of Starch Degrading Bacteria from Sago Industry Wastes

The sago processing industries generate high concentrations of organic pollutants. These industries required about 20,000 to 40,000 litres of water per ton of sago processing. They let out the water with hightoxic and organic matter causing serious threats to the environment and aquatic life. Potential starch degrading microorganisms are required to degrade the organic contaminants in the sago industry wastes before being generated. Sago wastes were collected from sago industries using sterilecans and polythene bags. The bacterial strains were obtained by adopting serial dilution methods and they were identified up to the generic level by their morphology and biochemical characteristics. The potential strains were screened by starch hydrolysis test and they were identified to the species level by 16s rDNA sequencing. The aligned sequences were evolutionary genetics analysis format using MEGA v.2. 1 software and construct phylogenetic trees using the neighbour-joining method and SDS-PAGE zymogram analysis starch degrading bacteria producing amylase enzyme.There are 103bacterial strains were isolated and identified. They were belonging to the genera of Bacillus (72%), Micrococcus (8%), Enterobacteriaceae (6%), Corneybacterium (5%), Aeromonas (4%), Alcalinges (3%) and Pesudomonas (2%). Among the isolates, there are 5 strains namely S5, S7, S16, S20 and S28 were selected as potential starch degraders. The database of the strains wassubmitted to the NCBI gen bank and got the accession numbers (S5-KY213660, KY213661, KY213662, KY230509 and KY230510). The molecular mass of the amylase was estimated to be ~45 kDa by SDS-PAGE and zymogram analysis. The strains S5, S7, S16, S20 and S28 showed more efficiency for the degradation of starch. These strains can be used to degrade starch from the waste substrates fabricating with amylase and glucose as the products. Key wordsSago effluent, waste water sediment, sago sludge, bagasse, tapioca peel.
Detection of Brucella in Tissues and in Formalin-Fixed Paraffin-Embedded (FFPE) Specimens Using PCR

| The present study investigated different diagnostic techniques for the detection of Brucella species in tissue specimens obtained from cattle including culturing technique, universal and Bruce ladder PCR assays based on fresh and formalin fixed paraffin embedding (FFPE) tissues as well as histopathological alterations. Specimens from 102 non-vaccinated brucella seropositive cows were used for isolation of brucellae. Brucella melitensis biovar 3 was isolated from 86 (84.31%) cows. Additionally, universal PCR showed the presence of Brucella DNA in all tissue extracts from which Brucella melitensis has been isolated as well as DNA extracts of their cultures. The assay has amplified the target gene (immunodominant antigen, gene bp26) with fragment size of 450 bp. Bruce ladder multiplex PCR proved the presence of genetic materials of Brucella melitensis in culture DNA extracts as it amplified three fragments (587, 1071 1682 bp in length). On the other hand, Bruce ladder multiplex PCR failed to detect DNA from fresh tissues. The use of FFPE technique on positive culture FFPE specimens, revealed the fingerprints of Brucella spp. DNA in udder, spleen, supramammary and retropharyngeal lymph node targeting 450 bp-fragment using the universal PCR. Moreover, Bruce ladder amplified only the 587 bp-fragment in only one (16.66%) sample out of 6 randomly selected positive universal PCR FFPE specimens. Pathological lesions in tissues of Brucella-infected animals consisted of micro-granulomatous reactions in lymph nodes and spleen. The current study tested brucellosis FFPE specimens and could effectively identify Brucella using specific primers by PCR. The immunodominant antigen, gene bp26, proved a good target for detection of DNA from FFPE tissues.
HISAT-genotype: Next Generation Genomic Analysis Platform on a Personal Computer

Rapid advances in next-generation sequencing technologies have dramatically changed our ability to perform genome-scale analyses of human genomes. The human reference genome used for most genomic analyses represents only a small number of individuals, limiting its usefulness for genotyping. We designed a novel method, HISAT-genotype, for representing and searching an expanded model of the human reference genome, in which a comprehensive catalogue of known genomic variants and haplotypes is incorporated into the data structure used for searching and alignment. This strategy for representing a population of genomes, along with a very fast and memory-efficient search algorithm, enables more detailed and accurate variant analyses than previous methods. We demonstrate HISAT-genotype’s accuracy for HLA typing, a critical task in human organ transplantation, and for the DNA fingerprinting tests widely used in forensics. In both applications, HISAT-genotype not only improves upon earlier computational methods, but matches or exceeds the accuracy of laboratory-based assays. One Sentence Summary HISAT-genotype is a software platform that has the ability to genotype all the genes in an individual’s genome within a few hours on a desktop computer.
The Role of the Pseudomonas aeruginosa 1244 Pilin Glycan in Virulence

The pili of P. aeruginosa 1244 are involved in a post-translational modification in which an acidic carbohydrate moiety structurally similar to the lipopolysaccahride (LPS) O-antigen is covalently attached to the pilin protein. It has been shown that this associated glycan is evenly distributed over the entire surface of the pilus. Because of its prime location along the pilus, experiments were conducted to determine if the pilin glycan contributed to the virulence of P. aeruginosa. Initial studies involved the assessment of LD50 values to demonstrate that acquisition of the exoU gene increased the virulence of PA1244. Interestingly, the LD50 studies suggested a role for the pilin glycan in PA1244 virulence. As a more sensitive determination of virulence, a competition assay utilizing a murine model of acute pneumonia demonstrated increased virulence associated with the glycan. Furthermore, employment of a nonopsonic phagocytosis assay has indicated inhibition of phagocytosis correlated with the pilin glycan.
Studies on 3H-levamisole binding to murine splenic lymphocytes, normal, malignant human lymphocytes and fate of levamisole in cell culture

Background: Levamisole at high concentrations has been shown to have anticancer and immunosuppressive actions. Methods: In the present study, fate of levamisole in cell culture and 3 H-levamisole binding to murine splenic lymphocytes, normal and malignant human lymphocytes has been investigated. Results: High-performance liquid chromatography analysis of cell culture supernatants of myeloma cells treated with levamisole has shown that products of levamisole appeared with progressive culture period indicating a metabolic transformation. 3 H-levamisole binding assays indicate that the binding was signifi cantly higher in lysates of lipopolysaccharide-stimulated murine splenic lymphocytes as compared to whole cells. Conclusion: The degradation of levamisole could be one more possible reason for the high concentration of levamisole required to get the desirable cytotoxic effect on myeloma cells.
The endocannabinoid anandamide and endometrial remodelling: importance of cyclooxygenase-2 metabolites

s in international peer-reviewed journals B. M. Fonseca, G. Correia-da-Silva, M. Almada, M.A. Costa, R. Ferreira and N. Teixeira “Characterization of the endocannabinoid system in telomerase-immortalized human endometrial stromal cell line, St-T1b. ” 2013 FEBS Journal, 280, Supp S1, 556-557.
PCR-RFLP ANALYSIS Of INSULIN-LIKE GROWTH FACTOR-I GENE IN BALI CATTLE

Penelitian ini bertujuan mengungkap polimorfisme gen insulin-like growth factor-I (IGF-I) pada sapi Bali menggunakan teknik PCR-RFLP. Apabila sifat polimorfik dari gen-gen ini dapat dideteksi maka efeknya terhadap pertumbuhan dapat dipelajari dan kemungkinan dapat dipergunakan sebagai marker genetik untuk seleksi pertumbuhan sapi Bali. Sampel darah diambil dari tiga populasi sapi Bali:sapi Bali di Pusat Perbibitan Sapi Bali (P3Bali) dan sapi Bali di luar wilayah P3Bali di pulau Bali maupun di luar pulau Bali (Kalimantan Selatan), berturut-turut sebanyak 111, 85 dan 46 sampel. Identifikasi polimorfisme gen IGF-I dilakukan dengan mendigesti fragmen DNA berukuran 249 bp yang berlokasi pada 5’-flanking region dari gen IGF-I menggunakan enzim SnaBI. Hasil penelitian menunjukkan bahwa pada ketiga populasi sapi Bali tersebut hanya ditemukan alel B, dan tidak ditemukan alel A atau alel lain. Disimpulkan bahwa gen IGF-I tidak bersifat polimorfik pada sapi Bali dan genotipe IGF-I adalah homosigot BB.
Homology modelling and in silico substrate-binding analysis of a Rhizobium sp. RC1 haloalkanoic acid permease

ABSTRACT Rhizobium sp. RC1 grows on haloalkanoic acid (haloacid) pollutants and expresses a haloacid permease (DehrP), which mediates the uptake of haloacids into the cells. For the first time, we report the homology model and docking analysis of DehrP and propose its putative binding residues. Ligand structures were retrieved from the ChemSpider database. The three-dimensional (3D) structure of DehrP was modelled based on the structure of Staphylococcus epidermidis glucose:H+ symporter (GlcPse) by Phyre2, refined by 3Drefine and evaluated by ProSA z-score, ERRAT and RAMPAGE. The 3D structure of the DehrP protein has 12 transmembrane helices. The overall quality factor of the model is ∼91%, with 93.6% of the residues in the favoured region and the z-score (−2.86) falls within the range (≤10) for a good model. Subsequent docking of monobromoacetate, monochloroacetate, dibromoacetate, dichloroacetate, trichloroacetate and 2,2-dichloropropionate ligands via AutoDock Vina1.1. 2 showed that residues Gln133, Asp36 and Arg130 are the putative H+-binding site, while the probable haloacid interacting residues are Glu33, Trp34, Phe37, Phe38, Gln165 and Glu370. The DehrP-haloacid complexes exhibited binding affinities between −2.9 and −4.0 kcal/mol. Both the putative H+ and haloacid-binding sites of DehrP possibly aided in co-transportation of substrates H+ and haloacids into the bacterial cells through the alternating access mechanism, which occurs by formation of halogen bonds and van der Waals interactions with the substrates. Hence, site-directed mutagenesis on the DehrP binding residues could improve the haloacid-binding affinity for efficient haloacid degradation.
Native and Invasive Woody Species Differentially Respond to Forest Edges and Forest Successional Age

Forest fragmentation can promote non-native plant invasions by increasing invasive plant seed dispersal and resource availability along edges. These effects can vary based on forest age and may be influenced by differences in traits of native and invasive plant species. To determine how native versus invasive plant species respond to forest edges and forest successional age, we experimentally evaluated germination, survival, and growth of three native and three invasive woody plant species in eastern USA forests. Across all species, increasing distance from the edge resulted in more germination and less seedling growth, but had no effect on seedling survival. Generally, seedling growth was greater in younger forests and invasive species outperformed native species; however, there were significant species-specific differences in performance. For example, among native species, spicebush had poor growth performance but high survival, while redbud had low germination but high growth performance and survival. By contrast, the invasive privet and autumn olive produced more biomass with high relative growth rates, and autumn olive had exceptionally high germination but the lowest survival. Overall, our results suggest that while there are some general characteristics of invasive species, species-specific traits may better inform management strategies and improve predictions about biological invasions along forest edges.
Development of a GFP Fluorescent Bacterial Biosensor for the Detection and Quantification of Silver and Copper Ions

Ionic silver is known to be an effective antimicrobial agent widely used in the cleaning and medical industries, however, there are several concerns regarding the release of silver pollutants into the environment. Presented here are two engineered bacterial biosensors for the detection and quantification of silver. The biosensors contain a silver resistance operon and a GFP gene that is strictly regulated through silver activated regulatory regions that control expression of the sil operons. The two biosensors are responsive to a wide range of silver ion concentrations, and a correlation between silver and GFP signal is seen at select concentration ranges. The biosensors were shown to detect silver ions released from silver nanoparticles, and have the potential to become a method for monitoring ion release rates of different nanoparticles. Interestingly, the close homology of the silver resistance and copper resistance genes allowed for the biosensor to also be responsive to copper ions, implying that copper ions activate silver resistance. Further development of this biosensor could lead to commercial applications for environmental monitoring. Importance Ionic silver is known to have many harmful environmental effects. Silver pollutants have been found in various environmental settings such as natural waterways and tailings from mining operations, raising concern. In addition, persistent exposure to silver in medical and environmental settings has led to the development of silver resistant bacteria, many of which are also resistant to a wide range of antibiotics. Some of these have the potential to develop into human pathogens. It then becomes important to have standardized methods for detecting and monitoring silver concentrations in various environments so that appropriate measures can be taken to prevent further silver ion release. This research shows that bacterial biosensors engineered to detect and quantify silver ions can be developed as effective alternatives to traditional analytical techniques. Further development of such biosensors could result in a commercial system for short and long term environmental monitoring, which is important as products containing silver and other heavy metals become increasingly popular.
Determining rewiring effects of alternatively spliced isoforms on protein-protein interactions using a computational approach

The critical role of alternative splicing (AS) in cell functioning has recently become apparent, whether in studying tissue-or cell-specific regulation, or understanding molecular mechanisms governing a complex disorder. Studying the rewiring, or edgetic, effects of alternatively spliced isoforms on protein interactome can provide system-wide insights into these questions. Unfortunately, high-throughput experiments for such studies are expensive and time-consuming, hence the need to develop an in-silico approach. Here, we formulated the problem of characterization the edgetic effects of AS on protein-protein interactions (PPIs) as a binary classification problem and introduced a first computational approach to solve it. We first developed a supervised feature-based classifier that benefited from the traditional features describing a PPI, the problem-specific features that characterized the difference between the reference and alternative isoforms, and a novel domain interaction potential that allowed pinpointing the domains employed during a specific PPI. We then expanded this approach by including a large set of unlabeled interactomics data and developing a semi-supervised learning method. Our method called AS-IN (Alternatively Splicing INteraction prediction) Tool was compared with the state-of-the-art PPI prediction tools and showed a superior performance, achieving 0.92 in precision and recall. We demonstrated the utility of AS-IN Tool by applying it to the transcriptomic data obtained from the brain and liver tissues of a healthy mouse and western diet fed mouse that developed type two diabetes. We showed that the edgetic effects of differentially expressed transcripts associated with the disease condition are system-wide and unlikely to be detected by looking only at the gene-specific expression levels.
Involvement of clock genes in seasonal, circadian and ultradian rhythms of Nasonia vitripennis

Natuurlijke selectie en overleving van de sterkste zijn belangrijke ingredienten voor evolutie. Een goede timing van activiteiten ten opzichte van de seizoenen, dagen en zelfs seconden is cruciaal voor overleving. Nasonia vitripennis is een parasiterende wesp die in staat is om activiteiten te timen op verschillende tijdschalen: een soort overwintereing genaamd diapauze (seizoensgebonden), dagelijkse activiteiten (circadiaan) en paringsinitiatie (ultradiaan). Noord Europese populaties van N. vitripennis gaan eerder in diapauze dan zuidelijke populaties en deze populaties verschillen ook in meerdere andere ritmische eigenschappen. De circadiane klok is mogelijk belangrijk voor het reguleren van siezoensgebonden diapauze omdat een klokgen, period, dat bekend is om zijn rol in de timing van dagelijkse activiteiten, is gecorreleerd met de verschillen in diapauze. Door het belang van period expressie op dagelijkse activiteiten, de expressie van andere klokgenen en paringsinitiatie te analyseren, heb ik twee modellen kunnen ontwerpen die verklaren hoe period betrokken kan zijn bij de timing van activiteiten op andere tijdschalen. Beide modellen ondersteunen de hypothese dat er een
Assessing potential Argentine Ant recruitment to pipping eggs in the Red-tailed Tropicbird on Rapa Nui (Easter Island)

ABSTRACT The invasive Argentine Ant, Linepithema humile, is known to prey on land bird chicks, but there are few reports of the ants’ impacts on breeding seabirds. We conducted a manipulative study using hen eggs to estimate the potential Argentine Ant recruitment to pipping eggs in the Red-tailed Tropicbird, Phaethon rubricauda, at Rapa Nui (Easter Island), Chile. Hen eggs were experimentally opened to simulate pipping eggs and control eggs were left unopened. The eggs were monitored for 90 min. The time elapsed until the arrival of the first ant did not differ between experimental and control eggs. None of the control eggs were visited by more than two ants. In contrast, the inferred cumulative number of ants that arrived at experimental eggs varied from 1 to >450. Simulated pipping eggs attracted a high number of ants in a short period of time, and the probability of an egg being attacked by ants after 5 and 60 min of exposure was 75% and 99%, respectively. A long-term monitoring study is needed to determine the actual Argentine Ant recruitment rate on pipping eggs, and the potential effects on the post-fledging survival rate of this native seabird which is threatened by a number of introduced species.
The alkyl side chain of PACA nanoparticles dictates the impact on cellular stress responses and the mode of particle-induced cell death

For optimal exploitation of nanoparticles (NPs) in biomedicine, and to predict nanotoxicity, detailed knowledge on the cellular responses to cell-bound or internalized NPs is imperative. The outcome of NP-cell interaction is dictated by the type and magnitude of the NP insult and the cellular response. Here, we have systematically studied the impact of minor differences in NP composition on cellular stress responses and viability by using highly similar poly(alkylcyanoacrylate) (PACA) particles. Surprisingly, PACA particles differing only in their alkyl side chains; butyl (PBCA), ethylbutyl (PEBCA), or octyl (POCA), respectively, induced different stress responses and modes of cell death in human cell lines. POCA particles induced endoplasmic reticulum stress and apoptosis. In contrast, PBCA and PEBCA particles induced lipid peroxidation by depletion of the main cellular antioxidant glutathione (GSH), in a manner depending on the levels of the GSH precursor cystine, and transcription of the cystine transporter SLC7A11 regulated by ATF4 and Nrf2. Intriguingly, these particles activated the recently discovered cell death mechanism ferroptosis, which constitutes a promising alternative for targeting multidrug-resistant cancer stem-like cells. Of the two, PBCA was the strongest inducer. In summary, our findings highlight the cellular sensitivity to nanoparticle composition and have important implications for the choice of PACA monomer in therapeutical settings.
Morphotaxonomy, distribution and abundance of Spirogyra (Zygnematophyceae, Charophyta) in Lake Baikal, East Siberia

Abstract: Some shallow-water zones of Lake Baikal have recently begun to show dramatic changes in phytobenthic communities. From 2012 to 2016, we studied species composition, distribution and abundance of Spirogyra, atypical of the open nearshore waters of Lake Baikal. In September 2014, Spirogyra dominated a considerable length of the coastal zone, extending the upper boundary of its previously known vertical distribution to above 0.5-m depth. Maximum algal biomass at this depth was at sites close to settlements and popular tourist destinations: 125.0 ± 59.0 and 70.5 ± 39.0 g m−2 (both n = 8) (Bol'shoye Goloustnoye village and 2 km south of the Tyya River) in the southern and northern basins, respectively. Based on morphology of fertile specimens, we identified 15 taxa, including one intraspecific form of Spirogyra from 37 lake sites and five streams. Eight taxa were new for Lake Baikal; nine were previously unknown for the region. Eight morphological species were reported for East Siberia for the first time. The species richness of the genus was higher in shallow-water bays with sandy bottoms in areas presumably influenced by organic pollution. The most common was S. cf. fluviatilis that developed year-round in the rocky Baikal littoral at 0.5–17.0-m depths and in one of the tributaries as well as in the Angara River. This study provides the first detailed account of the mass development of Spirogyra in Lake Baikal under conditions of an unfolding ecological crisis and the first data regarding species richness and distribution of Spirogyra in the Lake Baikal region.