Miracle-dz/UniFAR-FTUs huggingface dataset:
Impacts of manure application timing and tillage practices on antibiotic resistant bacteria and genes in drainage water from manured fields

Agriculture is an economic cornerstone in Iowa and the surrounding states, as well as arguably the entire United States as a whole. However, there is growing concern about the use of antibiotics in the animal agriculture sector and its contribution to antibiotic resistance (Levy & Marshall, 2004). Yet it is still unclear how antibiotic resistance is affected by environmental factors at the field scale and what mechanisms can be utilized to minimize the transport. This three-year study monitors both phenotypic and genotypic antibiotic resistance markers in subsurface drainage from research plots with varying manure application times and tillage practices. Enterococcus and tylosin and tetracycline-resistant Enterococcus were monitored as well as three antibiotic resistant genes (ermB, ermF, tetM) to 1) quantify antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in subsurface drainage 2) evaluate the impact of field management practices, manure application timing and tillage both the antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs), and 3) assess relationships between phenotypic and genotypic indicators of antibiotic resistance. Results of the study show overall low levels of both ARB and ARGs leading to further research questions with the targeted improvement of new methods. Although recommendations on specific field management practices best suited to minimize ARB and ARG transport cannot be drawn from the results of this study, it was shown that manure application in the spring had the strongest potential for future research.
Cellulolytic enzyme-producing thermophilic Actinobacteria isolated from the soil of Cisolok Geysers, West Java, Indonesia

Abstract. Setyaningsih PP, Ningsih F, Rachmania MK, Syafitri WA, Sari DCAF, Yabe S, Yokota A, Oetari A, Sjamsuridzal W. 2019. Cellulolytic enzyme-producing thermophilic Actinobacteria isolated from the soil of Cisolok Geysers, West Java, Indonesia. Biodiversitas 20: 3134-3141. This study investigated 17 thermophilic Actinobacteria isolated from the soil of geysers in the Cisolok geothermal area, West Java, as potential producers of cellulase. Screening for cellulase was performed on minimal (Mm) agar medium with and without the addition of 1% (w/v) carboxymethylcellulose (CMC) and microcrystalline cellulose (MCC), then incubated at 45, 50, 55 and 60°C for up to 7 days. Formation of clear zones around colonies indicated cellulose hydrolysis. The results showed that 15, 14, 4, and 3 isolates showed cellulolytic activity on CMC agar medium at 45, 50, 55, and 60°C, respectively, after 7 days of incubation. Three potential isolates showed cellulolytic activity on MCC agar medium after being incubated for 7 days at 45°C. Molecular identification based on the 16S rRNA gene was performed for three isolates with positive cellulolytic activity at 60°C. The results showed that the three isolates are closely related to Actinomadura keratinilytica WCC-2265T with 99.93-100% sequence similarities. A phylogenetic tree based on 16S rRNA gene sequences confirmed that the three isolates were clustered together with Actinomadura keratinilytica WCC-2265T with 100% bootstrap value. The tree also showed that cellulase producers and non-cellulase producers in Thermomonosporaceae are grouped into different clades.
Evolutionary consequences of fertilisation and early development in warming seas

Natural populations of plants and animals are experiencing stressful changes to their environments due to global warming, but may undergo evolutionary adaptation to counter these stressful conditions. My thesis aims to examine the capacity of marine invertebrate populations to adapt under future conditions, with particular focus on their most vulnerable life stages – fertilisation and early development. Through several empirical studies, I investigate whether populations have the genetic variation required for adaptation to projected levels of ocean warming, and explore which biologically-important traits will be involved in adaptation. My findings provide novel insights to help guide future conservation strategies.
Nova proteins direct synaptic integration of somatostatin interneurons through activity-dependent alternative splicing

Somatostatin interneurons are the earliest born population of cortical inhibitory cells. They are crucial to support normal brain development and function; however, the mechanisms underlying their integration into nascent cortical circuitry are not well understood. In this study, we begin by demonstrating that the maturation of somatostatin interneurons is activity dependent. We then investigated the relationship between activity, alternative splicing and synapse formation within this population. Specifically, we discovered that the Nova family of RNA-binding proteins are activity-dependent and are essential for the maturation of somatostatin interneurons, as well as their afferent and efferent connectivity. Within this population, Nova2 preferentially mediates the alternative splicing of genes required for axonal formation and synaptic function independently from its effect on gene expression. Hence, our work demonstrates that the Nova family of proteins through alternative splicing are centrally involved in coupling developmental neuronal activity to cortical circuit formation.
The Effect of Light-Emitting Diode Light on the Physical Traits of Chicks

Environmental conditions including light are considered a critical element of chicks well-being. The aim of the present study was to investigate the effect of LED light on the physical traits of chicks. We took forty-one-day-old chicks and randomly separated it into two groups. The chicks in the first group were reared under the effect of incandescent lamp light and in the second one were under the effect of white LED lighting. Chicks were daily monitored for individual chick body, weight gain, feed intake, feather color and fear responses. The distance between chicks and source of light was 50 cm. Student’s t-test test was used for statistical evaluation at p < 0.05 level. The results of the current study showed that chicks reared under incandescent light bulb had significantly higher body weight compared with chicks reared under LED light. The magnitude of body weight in LED group was lower (1192.75 ± 149.9 g) compared to incandescent light group (1307.75 ± 110.5 g). The obtained results revealed that LED light reared chicks were more active; it showed long mobility duration and high levels of exploration in the farm as compared to those in incandescent light group. The results also indicated that incandescent light chicks were less fearful than LED chicks. Furthermore, the study showed that LED light reared chicks have pale pink combs and white feathers that cover all over the body. On the other hand, incandescent light reared chicks have dark red combs and whitish-yellow feathers that cover certain areas of the body especially chick wings, tail and head.
Temperature and nutrient gradients correspond with lineage-specific microdiversification in the ubiquitous and abundant Limnohabitans freshwater genus

Most freshwater bacterial communities are characterized by a few dominant taxa, which are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic basis underlying this pattern is limited to a subset of taxa. Here, we investigated the genomic basis that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight metagenome assembled genomes (MAGs) from this genus along broad environmental gradients existing in Lake Michigan, part of Earth’s largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with co-occurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain-delineation had not previously been achieved. Our data show that temperature and nutrient levels may be two of the primary drivers of microdiversification within the Limnohabitans genus. Additionally, strains predominant in low and high phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with cultured Limnohabitans strains. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification, and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.
Methods in yeast genetics : a Cold Spring Harbor Laboratory course manual

Genetic nomenclature. Looking at yeast cells. Experiments: isolation and characterization of auxotrophic, temperature-sensitive, and UV-sensitive mutants meiotic mapping mitotic recombination and random spore analysis transformation of yeast cytoduction and karyogamy gene replacement isolation of ras2 suppressors manipulating cell types isolation of suppressors of telomeric silencing by insertional shuttle mutagenesis lacZ gene fusion expression in yeast immunofluorescent staining of yeast cells. Techniques and protocols: super-efficient transformation of yeast with lithium acetate/SS-DNA/PEG other yeast transformation methods yeast colony hybridization yeast DNA isolations yeast protein extracts yeast RNA isolation northern analysis - formaldehyde agarose gel, blotting, and hybridization to filters alkaline southern blotting procedure scoring killer factor hydroxylamine mutagenesis of plasmid DNA assay of galactosidase in yeast transformation of bacteria (CaC12 method) plate assay for carboxypeptidase western blotting protein extracts random spore analysis yeast vital strains yeast immunofluorescence with antibodies actin staining in fixed cells PCR analysis of genotype quick e coli plasmid DNA mini-prep. Appendices: media stock preservation yeast genetic map grids electrophoretic karotypes of strains for southern blot mapping strains counting yeast cells with a standard hemocytometer chamber.
Estrogen,Hormonal Replacement Therapy and Cardiovascular Disease

Premenopausal women have lower risk and incidence of hypertension and cardiovascular disease(CVD) compared to age-matched men and this sex advantage for women gradually disappears after menopause,suggesting that sexual hormones play a cardioprotective role in women.However,randomized prospective primary or secondary prevention trials failed to confirm that hormone replacement therapy(HRT) affords cardioprotection.This review highlights the factors that may contribute to this divergent outcome and could reveal why young or premenopausal women are protected from CVD and yet postmenopausal women do not benefit from HRT.
dSNE: a visualization approach for use with decentralized data

Visualization of high dimensional large-scale datasets via an embedding into a 2D map is a powerful exploration tool for assessing latent structure in the data and detecting outliers. It plays a vital role in neuroimaging field because sometimes it is the only way to perform quality control of large dataset. There are many methods developed to perform this task but most of them rely on the assumption that all samples are locally available for the computation. Specifically, one needs access to all the samples in order to compute the distance directly between all pairs of points to measure the similarity. But all pairs of samples may not be available locally always from local sites for various reasons (e.g. privacy concerns for rare disease data, institutional or IRB policies). This is quite common for biomedical data, e.g. neuroimaging and genetic, where privacy-preservation is a major concern. In this scenario, a quality control tool that visualizes decentralized dataset in its entirety via global aggregation of local computations is especially important as it would allow screening of samples that cannot be evaluated otherwise. We introduced an algorithm to solve this problem: decentralized data stochastic neighbor embedding (dSNE). In our approach, data samples (i.e. brain images) located at different sites are simultaneously mapped into the same space according to their similarities. Yet, the data never leaves the individual sites and no pairwise metric is ever directly computed between any two samples not collocated. Based on the Modified National Institute of Standards and Technology database (MNIST) and the Columbia Object Image Library (COIL-20) dataset we introduce metrics for measuring the embedding quality and use them to compare dSNE to its centralized counterpart. We also apply dSNE to various multi-site neuroimaging datasets and show promising results which highlight the potential of our decentralized visualization approach.
Multi-marker Study of Dreissena polymorpha Populations from Hydropower Plant Reservoir and Natural Lake in Latvia

Hydropower plants (HPPs) are equipped with reservoirs that can accumulate the toxic effluents and disturb the water flow of rivers. The aim of this study was to evaluate the biochemical responses of zebra mussel Dreissena polymorpha inhabiting the reservoir of Riga HPP in comparison with the responses of the mussels from the natural lake Kanieris in Latvia. In the reservoir mussels, high Mn-SOD activity and low level of the lipid peroxidation (production of TBARS) in the soft tissues suggested an elevated antioxidant activity. Compared to the lake specimens, the reservoir mussels had low levels of RI GSH while their lactate/pyruvate ratio was 1.4 times higher. In the mussels from the reservoir, high level of protein carbonilation products, as well as lowered caspase-3 and extralysosomal cathepsin D activities (by 1.4 and 1.6 times respectively, compared to the lake specimens) indicated delayed apoptosis. Catalase and glutathione S-transferase activities and metallothionein concentration were similar in both groups. Vitellogenin-like proteins (detected as the alkali-labile phosphates) and cholinesterase levels were higher in the mussels from the reservoir. We chose the indexes of the redox capacity as the most suitable markers of the environmental impact on this organism.
Human papillomavirus genotype distribution and co-infection with sexually transmitted pathogens in reproductive age women in urban Gambia

Cervical cancer is the second most common female cancer in The Gambia, and there have been few studies carried out on the causative agent, human papillomavirus (HPV) in this country. The Gambia introduced the quadrivalent HPV vaccine for girls between the ages of 9-13 years in the urban area in 2014; nationwide immunization will take place in 2019. This study determined the common circulating oncogenic HPV types in the urban region where most cervical cancer cases were reported. Two hundred and thirty-two women between 20 – 49 years of age from the urban region who attended a polyclinic were recruited for this work. Endocervical and high vaginal swabs were collected, and a socio-demographic questionnaire was administered to capture potential risk characteristics associated with HPV. Nucleic acid amplification techniques and DNA sequencing were carried out to determine the HPV genotype using PGMY09/11 consensus primers. Phylogenetic analysis was carried out on the Gambian HPV sequences to further confirm the identification of The Gambian HPV genotypes and its relatedness to sequences of the same types from other geographical locations. Microbiological and nucleic acid amplification analyses were used to determine the prevalence of other sexually transmitted pathogens in the participants. Blood samples, endocervical swab, and Pap smear were collected from HIV positive participants and these participants were followed up and re-examined every nine months for 24 months, to determine the persistence of cervical HPV infection, HPV antibodies, and cytological cervical changes. Pseudo-typed neutralisation assays were performed to characterise high-risk HPV antibodies in HIV positive women. Among the sample population studied, HPV prevalence was found to be 12% (28/232). HPV 52 was the most prevalent (17.9%) genotype detected in cervical samples. The Gambian high-risk HPV genotypes, except for a novel putative HPV 35 genotype, were 98 -100% identical to those submitted in the GenBank database. Prolonged (> 5 years) use of hormone contraceptive was the only variable found to associate statistically with HPV infection. Fifty percent (14/28) of participants infected with HPV were co-infected with Ureaplasma urealyticum/parvum and 25% (7/28) with HIV. HPV sero-prevalence was found to be 51.7% (15/29) in HIV positive participants. HIV positive women had been exposed to multiple HPV types and HPV 52 antibody was more prevalent 24% (7/29). Other high-risk HPV genotypes were found to cause high-grade cervical lesions and cancer in HIV positive women. Future studies to investigate oncogenic HPV genotypes in cervical cancer specimens will be useful in providing evidence for policies and future evaluation of the quadrivalent HPV vaccine in The Gambia.
Proximate and Ultimate Consequences of Stressed-Induced Maternal, Paternal, and Joint Parental Effects in a Changing World

Parental experience can alter the developmental and rearing environments of offspring, resulting in parental effects on offspring traits. I addressed the consequences of stress-induced maternal, paternal, and joint parental effects from both ultimate (ecological/evolutionary) and proximate (physiological/epigenetic) perspectives. I used a full-factorial design in which threespine stickleback (Gasterosteus aculeatus) mothers, fathers, both, or neither were exposed to a model predator at developmentally appropriate times to test for predator-induced maternal, paternal, and joint parental effects on daughters’ mating behavior and egg glucocorticoids (stress hormones) and on offspring gene expression. Maternal and paternal predator exposure independently yielded daughters who preferred less conspicuous mates with duller nuptial coloration and who courted less vigorously, relaxing (paternal) or reversing (maternal) typical preference for conspicuous males. The combined effects of maternal and paternal predator exposure were not cumulative; when both parents were predator-exposed, single-parent effects on daughters’ mate preferences were reversed. Therefore, parental effects may alter the direction of sexual selection. I tested the concentration of glucocorticoids, specifically cortisol, in the eggs of daughters post-mating trial using an enzyme-linked iii immunosorbent assay (ELISA). Daughters of predator-exposed parents (both parents exposed to model predator) had higher glucocorticoid concentrations in their eggs than daughters of control, unexposed parents. Daughters of predator-exposed mothers-only and predator-exposed fathers-only did not differ from control or jointly predator-exposed parents’ daughters. Therefore, predator-induced parental effects impact the gametes of their daughters, suggesting a mechanism through which predation risk may indirectly influence the next generation (grand-offspring). Finally, offspring gene expression varied with the source of parental effects: maternal and paternal effects on offspring gene expression were similar to each other, but each was different from joint parental effects. There were no differences in offspring gene expression when parent and offspring matched and mismatched (when offspring did or not experience direct predation risk themselves), perhaps because of the animals’ age at direct exposure and the specific method of predator-exposure used in this study. Maternal and paternal effects appear to be underlain by different epigenetic changes that yield independent, but perhaps additive, variation to offspring gene expression that could have an array of impacts on offspring phenotypes. Thus, stress-induced maternal, paternal, and joint parental effects may potentiate rapid transgenerational responses to novel and changing environments.
Allometric equations to estimate the above-ground biomass of trees in the tropical secondary forests of different ages

Abstract. Karyati, Ipor IB, Jusoh I, Wasli ME. 2019. Allometric equations to estimate the above-ground biomass of trees in the tropical secondary forests of different ages. Biodiversitas 20: 2427-2436. The allometric equations for trees of secondary forests of different ages in abandoned lands after shifting cultivation are still rarely available. The objective of this study was to develop allometric equations to estimate the above-ground biomass (AGB) of trees (DBH of > 5 cm) in the tropical secondary forest of different ages, namely 5, 10, and 20 years after abandonment. The selected trees in this study represented the dominant and rare species and DBH classes in each study site. The trunk dry biomass and AGB showed strong correlations (adjusted R2= 0.59-0.95) with diameter at breast height (DBH) and height. The leaf and branch dry biomass had weak correlations with height (adjusted R2=0.36-0.50). The developed allometric equations were suitable for trees of secondary forests of different ages, because the selected samples used in the destructive method were based on a field inventory data of forest structure and floristic composition.
Microbial communities in the estuarine water areas of the rivers in the southeastern part of Lake Baikal

Using the Illumina MiSeq platform, we have studied the diversity of bacteria and archaea in three rivers of the southeastern end of Lake Baikal in the under-ice period of 2018. In analysed 16S rRNA gene libraries of all rivers, we have identified sequences of 12 bacterial phyla: Actinobacteria, Bacteroidetes, Cyanobacteria, Elusimicrobia, Epsilonbacteraeota, Fibrobacteres, Firmicutes, Omnitrophicaeota, Patescibacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia. The contribution of minor taxa to the microbiomes from the estuaries of the rivers Solzan and Bolshaya Osinovka is more significant. Three phyla (Thaumarchaeota, Euryarchaeota and Crenarchaeota) and one superphylum (DPANN) represent archaea. The diversity of bacteria and archaea in the investigated ecotopes has its specifics and is not identical to that found in the pelagic zone of Southern Baikal. Bacteria show phylogenetic diversity at the level of families and genera, whereas archaea – at the level of phyla. In the microbiomes, we have identified microorganisms involved in various stages of transformation of organic and inorganic substances.