Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Biological Methods in Environmental Engineering

The “omics” revolution has enabled the development of tools for studying structural, functional, and informational macromolecules, as well as metabolites produced by cells under specific environmental conditions. Recent advances in molecular biological methods have facilitated their widespread applications in characterizing microbes in engineered and natural environments, exploring production of biofuels, and optimizing biological processes to improve the performance of wastewater treatment or subsurface remediation systems. Real‐time quantitative polymerase chain reaction (qPCR) is a rapid and versatile method of choice for the detection and quantification of microorganisms. Techniques such as cloning, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA), and microarrays continue to be popular tools to profile microbial community population and diversity in various environments over time and space. Gene expression can be linked to microbial functions for incorporation into predictive fate and transport models. This review summarizes new or significantly revised methods, novel applications of existing methods, and a few high impact studies using advanced molecular methods published after August 2010. New nucleic acid‐based methods, detection methods and sensors, and data analysis techniques are also highlighted. This review will serve environmental engineering professionals and microbiologists by providing an overview of recent advances in molecular methods, and their advantages and challenges in bioreactors and in‐situ applications.
Social learning and the significance of mixed-species flocks of chickadees (Parus spp.)

The experiments described in this paper show that two species of chickadees learn from one another about the location and nature of potential feeding places when they are foraging together in mixed flocks in large aviaries. In the first experiment, I show that when an individual of one species finds a single food item, members of the other species modify their foraging behavior over the next few seconds so that they put more effort into searching near the site of the find. This applies to both species. Further, members of both species modify their foraging behavior when a bird of the other species searches in a place unsuccessfully. This response to an unsuccessful search is similar to, but weaker than, the response to a food find. The second experiment shows that when the two species are trained to forage in different positions in the experimental trees, they converge in their foraging behavior when they are put in mixed flocks, This is a result of copying. The third experiment shows that individuals of .
La résistance du VIH : des premières générations d’inhibiteurs non nucléosidiques de la transcriptase inverse (INNTI) aux nouvelles générations

Les caracteristiques de la resistance aux inhibiteurs non-nucleosidiques de la transcriptase inverse (INNTI) de premiere generation, la nevirapine et l’efavirenz, sont la selection rapide de virus porteurs d’une ou plusieurs mutations dans le gene de la transcriptase inverse (TI), conduisant d’emblee a une resistance de haut niveau et croisee pour les deux composes. Ces mutations ont ete decrites proche du site de fixation des INNTI et aussi dans le domaine de connexion de la TI. Elles induisent une perte d’affinite de l’inhibiteur pour la cible sans alterer la capacite replicative des virus. Comme une seule mutation suffit a conferer un niveau eleve de resistance, la transmission de virus resistants aux INNTI, de l’ordre de 2 a 7 %, est fortement associee a l’echec virologique d’un traitement incluant des INNTI. Le developpement de nouveaux INNTI de seconde generation etait un reel enjeu. Ces composes, l’etravirine et la rilpivirine, sont tres actifs sur des virus porteurs de mutations et possedent une barriere genetique elevee. Les donnees de resistance de l’etravirine chez des patients pre-exposes aux INNTI de premiere generation montrent que parmi treize mutations sur le gene de la TI, au moins trois sont necessaires pour diminuer l’activite de l’etravirine. Des etudes recentes de prevalence de la resistance dans de grandes bases de donnees de patients pretraites par nevirapine et efavirenz dans les pays du Nord et du Sud rapportent une proportion importante des souches encore sensibles a l’etravirine (>75 %). Les premieres donnees de resistance pour la rilpivirine sont encourageantes mais encore tres limitees chez les patients naifs d’INNTI.
Prevalence and clonality of extended-spectrum β-lactamases in Asia

Asia is almost certainly a part of the world in which extended-spectrum beta-lactamases (ESBLs) have emerged de novo, with some early antimicrobial resistance studies showing high levels of the ESBL phenotype, particularly among Klebsiella, and most notably in China, Korea, Japan and India. There is a lack of genotyping studies but work from the late 1990s suggests that SHV-5 and SHV-12 were most common then, with only very rare reports of TEM-related ESBL genes. As in other parts of the world, quite marked differences have since been seen in the pattern of ESBL genes, particularly in relation to the CTX-M family. The early emergence of TOHO CTX-M-2 in Japan contrasted with CTX-M-3 and -14 in China and many other parts of the Far East, suggesting the separate transfer of genes from the genome of Kluyvera spp. to mobile genetic elements in human-associated Enterobacteriaceae. ESBL production rates are now very high compared with Europe. In most countries, there are mixtures of CTX-M types, with VEB appearing significantly in Vietnam and Thailand, and ESBL isolates from India being completely dominated by the presence of bla(CTX-M-15) alone, with no other CTX-M types reported. With the total population of India and China being c. 2.4 billion and with faecal carriage rates of, probably, c. 10%, these countries represent major reservoirs of bla(CTX-M) genes. Increasing international travel and trade will lead to the movement of many of these ESBL genes. The high prevalence of ESBL genes in Asia means that the empirical treatment of serious infections with beta-lactam antibiotics, except carbapenems, is seriously compromised.
Biology of odoriferous defensive stink glands of the red flour beetle Tribolium castaneum

Chemical warfare is a very common defense strategy in the insect world. A broad range of coleopteran beetles react to predators, invaders, and parasitic microbes with the release of toxic and repellent substances, which are synthesized in specialized secretory organs, referred to as odoriferous defensive stink glands. The worldwide known pest beetle Tribolium castaneum (Coleoptera: Tenebrionidae) uses these glands to produce antimicrobial p-benzoquinones and 1-alkenes. The stink gland morphology has been studied in detail in other tenebrionid beetles in the past, but to date only little is known about the genes involved in the biochemical processes of gland secretion production. Here, I present first transmission electron microscopic pictures of T. castaneum stink gland cells and a subset of genes required for proper benzoquinone production. I selected 59 potential candidates from a genome-wide RNAi knockdown screen named “iBeetle” and 12 genes based on the analysis of 11 stink gland-related Gal4 enhancer trap lines. All 71 candidate genes were functionally characterized by RNAi-mediated gene knockdown. 34 of them were found to cause stink gland phenotypes upon knockdown and were therefore selected for a subsequent gas chromatography-mass spectrometry (GC-MS) analysis of secretion volatiles in respective RNAi knockdown glands. In total, I identified 14 candidate genes that displayed strongly altered glands in terms of secretion color and chemical composition upon knockdown, revealing their involvement in secretion biosynthesis. Three of them play an essential role specifically in benzoquinone biosynthesis. Based on stink gland transcriptome data, I additionally analyzed the function of four glucosidases, eleven peroxidases, as well as four phenoloxidases via RNAi-mediated gene knockdowns. Morphologically altered stink glands were found for one peroxidase (Peroxiredoxin 3, Prxd3) and two phenoloxidases (Tyrosinase 1, Tyr1; Laccase 2, Lac2). Subsequent GC-MS analysis of secretion volatiles revealed reduced benzoquinone levels in Prdx3 and Tyr1 knockdowns and a complete lack of benzoquinones in the knockdown of Lac2. For Lac2, I could detect its expression in a certain subgroup of secretory stink gland cells and confirm its involvement in p-benzoquinone biosynthesis by enzymatic activity assays on stink gland tissue. This indicates a so far unidentified role of the cuticle tanning phenoloxidase Lac2.
When Protecting One Species Hurts Another

CONSERVATION BIOLOGYSWAN VALLEY, MONTANA-- Biologists studying whether providing habitat for one wide-ranging species would protect another--the so-called umbrella effect--have found limited overlap between prime grizzly habitat and that of threatened fish, and grizzly conservation programs here may even be hurting the fish. Researchers are now grappling with how best to conserve habitat for multiple species.
Evolutionary history of Apocheima cinerarius (Lepidoptera: Geometridae), a female flightless moth in northern China

The alterations in the phylogeographical structures of insects in response to the uplift of the Qinghai–Tibet Plateau and the Quaternary glaciations in eastern Asia, particularly in northern China, remain largely unknown. In this study, we selected Apocheima cinerarius, a moth with flightless females, using molecular data (complete mitochondrial genomes and nuclear data) and ecological niche modelling (ENM) to investigate the effects of paleoclimatic changes on the evolutionary history of insects in the area of northern China. The phylogenetic tree of complete mitochondrial genomes indicated that there were two lineages, the western and eastern lineages. The nuclear gene analyses also detected unique haplotypes in each lineage. Time of the most recent common ancestor (TMRCA) of the two lineages was approximately in Early–Middle Pleistocene. Bayesian skyline plots revealed that the western lineage underwent a population expansion event after the Last Glacial Maximum, whereas the eastern lineage underwent expansion between the Last Interglacial and the Last Glacial Maximum. Our results suggest that A. cinerarius expanded eastward from western sites until the moth was distributed across the entire region of northern China. Then, A. cinerarius underwent contraction into isolated glacial refugia followed by subsequent expansion driven by Pleistocene climate changes, which established a narrow sympatric area. Our results indicate that the Quaternary environmental fluctuations had profound influences on the diversification and demography of an insect in northern China, and the same species in north‐western China and north‐eastern China have different demographic histories.
Utilização de fosfatos comerciais para frangos de corte na fase inicial

The objective of this work was to evaluate the performance and the bone mineralization of broilers, at 1 to 21 days of age, and the bioavailability of phosphorus in commercial phosphates utilized in the broilers feeding. One thousand and eight male chickens of one day old were distributed in a completely randomized design, in fourteen treatments, with six replications of twelve birds each. Phosphates evaluated were: defl uorinated phosphate, monocalcium B, dicalcium A, dicalcium B and dicalcium C, with two levels of available phosphorus (0.30 and 0.40%). For the evaluation of the relative bioavailability, the abscissa technique was used, and the monocalcium A phosphate was taken as standard (value of 100%), with four levels of available phosphorus: 0.25, 0.35, 0.45 and 0.55%. All the phosphates with 0.40% of available phosphorus levels propitiated similar weight gain to broilers. The monocalcium B resulted in higher bone mineralization of broilers than the defl uorinated phosphate. The different phosphorus sources presented few differences in the values of relative bioavailability of phosphorus, with better results for the monocalcium B and with higher sensibility response for bone ashes than for body weight gain.
De la nécessité de redécrire les phéromones sexuelles des mâles de bourdons [Hymenoptera : Apidae, Bombini] publiées avant 1996 pour leur utilisation en analyse phylogénétique

Les auteurs comparent les descriptions des pheromones sexuelles des mâles de bourdons publiees avant et depuis 1996. Ils mettent en evidence une importante difference dans la quantite de molecules decrites entre ces etudes. Cette difference s’explique notamment par l’importante evolution dans l’informatisation des donnees et de leur analyse. Elle s’explique egalement par les objectifs des premieres etudes, limitees alors a decrire et a demontrer la specificite de ces pheromones. Les etudes menees depuis 1996 montrent que la majorite des molecules secretees sont presentes sous forme de traces. Neanmoins, ces molecules sont d’importance majeure pour toute etude entrant dans le concept moderne d’analyse phylogenetique globale («total evidence approach»). La redescription complete de ces pheromones pour les especes etudiees avant 1996 apparait donc indispensable.
Phylogeny, diversity, and classification of the Accipitridae based on DNA sequences of the RAG-1 exon

The avian family Accipitridae has historically been divided into subfamilies or tribes based on features such as general resemblance, feeding ecology, and behavior. Consequently, the monophyly of those groups has been questionable. Recently, three phylogenetic analyses of a majority of the genera have appeared, one based on osteology, one on DNA sequences from a single mitochondrial gene, and the third on mitochondrial plus nuclear DNA sequences, and the resulting phylogenies were in substantial disagreement concerning the composition and basal branching patterns of the clades and hence require further analysis and confirmation. Here we use DNA sequences from the large nuclear RAG-1 exon to investigate the phylogenetic relationships of these birds. Our results largely corroborated the prior study that included nuclear genes. We found strong support for a monophyletic clade comprising the secretarybird Sagittarius serpentarius, the osprey Pandion haliaetus, and the traditional accipitrids. However, every one of the traditionally recognized subfamilies of accipitrids was found to be polyphyletic. The most basal nodes in the phylogeny separate small clades of insectivorous and scavenger species, such as kites and Old World vultures, from the rest of the family. The speciose genera of bird and mammal predators are all relatively derived (terminal) in the phylogeny. Many of the basal clades are cosmopolitan in their distributions, consistent with the great mobility of these raptors. A new classification is proposed that eliminates the problem of polyphyletic intrafamilial taxa.
Evaluation of meat quality after application of different feed additives in diet of broiler chickens.

The present study was conducted to investigate the effect of natural feed additives, namely bee pollen extract, propolis extract and probiotic preparation, on technological properties of meat in order to evaluate the meat quality of Ross 308 broiler chickens. The feeding of chickens (180 pcs) lasted for a period of 42 days. The experiment was carried out without segregation between the genders. The chickens were randomly divided into 4 groups. The control group was fed a basal diet, whereas the other three groups were fed diets supplemented with natural additives, i.e. bee pollen extract at level of 400 mg.kg -1 of feed mixture, propolis extract at level of 400 mg.kg -1 of feed mixture, and probiotic preparation based on Lactobacillus fermentum (1.10 9 CFU per 1 g of bearing medium) in an amount of 3.3 g added to water (for 30 pcs chickens until 21 days of age, for 20 pcs chickens from 22 nd to 42 nd day of age) given to group E1, group E2 and group E3, respectively. The feed mixtures were produced without any antibiotic preparations and coccidiostatics. During the whole period of experiment, the broiler chickens had ad libitum access to feed and water. The following technological properties were examined: cooling loss (after 24 h of storage at 4 °C), freezing loss (after 3 months of storage at -18 °C), roasting loss (performed on roasted meat that was stored at -18 °C for 3 months before thawing), colour parameters based on CIELab system (the L*, a*, b* values of raw breast and thigh muscle), and tenderness (as shear force of roasted breast and thigh muscle). We have made a finding, that the examined additives had only little impact on meat quality in most of the investigated parameters, except the significant increase ( p ≤0.05) in redness (a*) values and the slight decrease in roasting loss and shear force determination after propolis extract supplementation. Therefore, it may be inferred that propolis extract has been shown as the most appropriate feed additive among the applied supplements.
DETECTION OF SELF-FERTILE ISOLATES OF PHYTOPHTHORA INFESTANS IN INDIA

Until 1984, Phytophthora infestans, the incitant of potato late blight, was known to reproduce sexually only in Mexico where both A 1 and A 2 mating types existed in equal proportion. With the appearance of A2 type in 1984 in Europe and in 1990 in India, the possibility of pathogen’s sexual reproduction and oospore formation arose. Oospores of P. infestans were recorded in spring season in nature and in culture of single isolate. Studies here aimed to monitor the fungus population for oospore formation and possibility of its survival in soil. Blighted foliage and stems were collected from the fields during November to April from 1999 to 2004 and inoculated in tubers. Isolations from inoculated/infected tubers and also from fresh diseased foliage collected from fields were made on Pea agar media. The culture was incubated at 18±1oC for observing pathogen’s growth and cultures were observed under microscope to see whether oospores were found or not. Isolates forming oospores, irrespective of their number, were identified as self-fertile and those without oospores regarded either of A 1 or A 2 strain after pairing with known tester. Out of 54 isolates obtained during the course of study from 1999 to 2004, 16 (29.62%) were observed forming oospores and identified as self-fertile. Remaining isolates belonged to either A 1 or A 2 mating types. A 2 type was predominant till 2001 (80%) whereas the native population A1 again dominated during 200304. Pathogenicity tests of self-fertile isolates conducted on detached leaves of cvs. Kufri Chandramukhi and Kufri Jyoti gave positive reaction. The critical examination of self-fertile isolates revealed that oospore formation initiated in 8 days period and one month old cultures revealed abundant oospores. The self-fertile isolates have also been reported to occur in England and in United States. The occurrence of self-fertile isolates during the present studies suggests the increased possibility of oospore formation in the region leading to greater genetical diversity in P. infestans population and also pathogen’s ability to over-summer in soil. The findings could be of significance in< developing strategies for the effective management of late blight.
Epidemiological modeling of invasion in heterogeneous landscapes: spread of sudden oak death in California (1990–2030)

The spread of emerging infectious diseases (EIDs) in natural environments poses substantial risks to biodiversity and ecosystem function. As EIDs and their impacts grow, landscape- to regional-scale models of disease dynamics are increasingly needed for quantitative prediction of epidemic outcomes and design of practicable strategies for control. Here we use spatio-temporal, stochastic epidemiological modeling in combination with realistic geographical modeling to predict the spread of the sudden oak death pathogen (Phytophthora ramorum) through heterogeneous host populations in wildland forests, subject to fluctuating weather conditions. The model considers three stochastic processes: (1) the production of inoculum at a given site; (2) the chance that inoculum is dispersed within and among sites; and (3) the probability of infection following transmission to susceptible host vegetation. We parameterized the model using Markov chain Monte Carlo (MCMC) estimation from snapshots of local- and regional-scale data on disease spread, taking account of landscape heterogeneity and the principal scales of spread. Our application of the model to Californian landscapes over a 40-year period (1990–2030), since the approximate time of pathogen introduction, revealed key parameters driving the spatial spread of disease and the magnitude of stochastic variability in epidemic outcomes. Results show that most disease spread occurs via local dispersal (<250 m) but infrequent long-distance dispersal events can substantially accelerate epidemic spread in regions with high host availability and suitable weather conditions. In the absence of extensive control, we predict a ten-fold increase in disease spread between 2010 and 2030 with most infection concentrated along the north coast between San Francisco and Oregon. Long-range dispersal of inoculum to susceptible host communities in the Sierra Nevada foothills and coastal southern California leads to little secondary infection due to lower host availability and less suitable weather conditions. However, a shift to wetter and milder conditions in future years would double the amount of disease spread in California through 2030. This research illustrates how stochastic epidemiological models can be applied to realistic geographies and used to increase predictive understanding of disease dynamics in large, heterogeneous regions.