Miracle-dz/UniFAR-FTUs huggingface dataset:
Study of Bacterial Motility Using Optical Tweezers

Bacteria are arguably the simplest of known microorganisms, forming a fundamental part of the world we live in. Many functions they perform are found in scaled-up versions in higher organisms. Among many advanced functions, bacteria possess the ability to move in search for nutrients and favorable growth conditions. Measurement of the dynamical variables associated with bacterial swimming has proven to be difficult due to the lack of an accurate and convenient tool. In the past optical traps have been used for the manipulation of microscopic objects and measurement of minute forces. Herein, I have devised techniques for use of optical traps for direct measurement of the dynamics of bacterial swimming and chemotaxis, shedding light on the propulsion apparatus and sensory systems. A detailed analysis is performed to explore the effects of non-local hydrodynamic interactions on the swimming of single cells. Due to the lack of reliable measurement techniques, experimentalists often use theoretical models to estimate bacterial dynamics, the validity of which are tested. I emphasize the shortcomings of the very popular Resistive Force Theory (RFT) and indicate how the more rigorous Slender Body Theory (SBT) is able to overcome the limitations. In addition the chemotaxis of the marine bacterial strain Vibrio alginolyticus is studied with the revelation of a previously unknown chemotactic mechanism. Direct observations showed that these cells are able to bend their flagella to impart direction changes, which is paramount for an effective search strategy. This interesting find opens several intriguing questions pertaining to chemotaxis.
Characterization of Mitochondrial Proteomic Changes in Resistant Wheat Near‐Isogenic Line After Inoculation with Powdery Mildew

Wheat powdery mildew resistance mechanisms have been studied extensively at genomic level, however, infection induced mitochondrial proteomic changes in resistant line have not been fully characterized. Being critical organelles of chemical energy metabolism, mitochondria have also been suggested to be involved in the environmental stress response. Using proteomic approaches, we did comparative analysis of mitochondrial proteome in resistant wheat near-isogenic line (NIL) (Brock 9 Jing411 7 ) and its recurrent parent Jing 411 after infection of Blumeria graminis f.sp. tritici (Bgt). More than 50 down-regulated mitochondrial protein spots were identified in NIL after 24-h pathogen inoculation, and their abundance recovered to the levels prior to infection after extended inoculation (72-h). We further analyzed a subgroup of down-regulated proteins using mass spectrometry. MS/MS data analysis revealed the identities of nine protein spots and assigned them into three functional classes: synthesis of protein, disease resistance response and energy metabolism. For the first time we demonstrated pathogen stress induced mitochondrial proteomic changes and provided evidences that wheat powdery mildew resistance involves multiple biochemical events. Moreover, our results indicate that wheat mitochondrial proteome analysis can serve as a powerful tool to identify potential regulators of fungal invasion resistance.
WINTER FORAGING OF LONG-TAILED DUCKS (CLANGULA HYEMALIS) EXPLOITING DIFFERENT BENTHIC COMMUNITIES IN THE BALTIC SEA

Abstract We studied the feeding ecology of Long-tailed Ducks (Clangula hyemalis) in two different marine benthic habitats in the Baltic Sea to determine whether there were differences in diet choice, foraging selectivity, body condition, and bird abundance. Our results corroborate earlier suggestions that Long-tailed Ducks exhibit ecological plasticity in selecting winter habitat and food. The majority of Long-tailed Ducks occurred in hard-bottom habitats where they relied on the bivalve Mytilus edulis; however, some of the population wintered in less productive, soft-bottom habitats where they employed a prey-selective foraging strategy, in which they fed on less abundant, but energy rich, crustaceans. Both strategies were apparently viable, as dissected birds in both habitats were in good body condition and had substantial fat reserves.
Interactive effects of ocean acidification and temperature on two scleractinian corals from Moorea, French Polynesia

This study tested the hypothesis that the response of corals to temperature and pCO 2 is consistent between taxa. Juvenile massive Porites spp. and branches of P. rus from the back reef of Moorea were incubated for 1 month under combinations of temperature (29.3 °C and 25.6 °C) and pCO 2 (41.6 Pa and 81.5 Pa) at an irradiance of 599 μmol quanta m−2 s−1. Using microcosms and CO2 gas mixing technology, treatments were created in a partly nested design (tanks) with two between‐plot factors (temperature and pCO 2), and one within‐plot factor (taxon); calcification was used as a dependent variable. pCO 2 and temperature independently affected calcification, but the response differed between taxa. Massive Porites spp. was largely unaffected by the treatments, but P. rus grew 50% faster at 29.3 °C compared with 25.6 °C, and 28% slower at 81.5 Pa vs. 41.6 Pa CO2. A compilation of studies placed the present results in a broader context and tested the hypothesis that calcification for individual coral genera is independent of pH, [HCO3 −], and [CO3 2−]. Unlike recent reviews, this analysis was restricted to studies reporting calcification in units that could be converted to nmol CaCO3 cm−2 h−1. The compilation revealed a high degree of variation in calcification as a function of pH, [HCO3 −], and [CO3 2−], and supported three conclusions: (1) studies of the effects of ocean acidification on corals need to pay closer attention to reducing variance in experimental outcomes to achieve stronger synthetic capacity, (2) coral genera respond in dissimilar ways to pH, [HCO3 −], and [CO3 2−], and (3) calcification of massive Porites spp. is relatively resistant to short exposures of increased pCO 2, similar to that expected within 100 y.
Aging and Gene Expression in the Primate

It is well established that gene expression levels in many organisms change during the aging process, and the advent of DNA microarrays has allowed genome-wide patterns of transcriptional changes associated with aging to be studied in both model organisms and various human tissues. Understanding the effects of aging on gene expression in the human brain is of particular interest, because of its relation to both normal and pathological neurodegeneration. Here we show that human cerebral cortex, human cerebellum, and chimpanzee cortex each undergo different patterns of age-related gene expression alterations. In humans, many more genes undergo consistent expression changes in the cortex than in the cerebellum; in chimpanzees, many genes change expression with age in cortex, but the pattern of changes in expression bears almost no resemblance to that of human cortex. These results demonstrate the diversity of aging patterns present within the human brain, as well as how rapidly genome-wide patterns of aging can evolve between species; they may also have implications for the oxidative free radical theory of aging, and help to improve our understanding of human neurodegenerative diseases.
EFFECTS OF OLD WORLD BLUESTEM (BOTHRIOCHLOA ISCHAEMUM) ON FOOD AVAILABILITY AND AVIAN COMMUNITY COMPOSITION WITHIN THE MIXED-GRASS PRAIRIE

Abstract Various grassland bird species have displayed population declines over the past 30 to 40 years, and interest in explaining possible causes for the declines has prompted numerous studies. Many of these studies have focused on changes in agricultural practices; few have evaluated possible effects of the presence of nonnative grasses in grasslands. The objective of our study was to determine the effects a nonnative grass, Old World bluestem (OWB; Bothriochloa ischaemum), might have on grassland bird species abundance and richness, and on bird food availability (arthropod biomass). Three pastures each of native range, expired Conservation Reserve Program (CRP), and OWB were sampled from May to July 2001 in Comanche County, Kansas. Bird abundance and species richness were assessed by using a point-count method along 3 transects in each pasture. Food availability was estimated by collecting arthropods along 10 transects in each pasture by sweep-netting. Results showed significantly lower bird abundance and species richness in OWB pastures than in native pastures. OWB pastures also had significantly less arthropod biomass than native pastures. Because food availability (arthropod biomass) was directly related to percent forb cover within fields and was mostly absent in OWB pastures, we contend these were the primary factors contributing to lower avian richness and abundance in OWB fields when compared to CRP and native pastures.
A lipidomics approach to the viral-host dynamics of the unicellular, eukaryotic alga cChlorella variabilis and its viral pathogen, PBCV-1

Sterols are essential molecules found in nearly every eukaryotic cell membrane. Having the unique ability to partner with sphingolipids, together they maintain the integrity, fluidity and permeability of cell membranes through the formation of detergent-resistant lipid rafts. Most eukaryotes and some prokaryotes encode the enzymatic genes required for sterol biosynthesis. Non-photosynthetic eukaryotes, animals and fungi, follow a different biosynthetic pathway than that found in plants or photosynthetic eukaryotes. The major sterols produced in nonphotosynthetic organisms are cholesterol and ergosterol, in animals and fungi, respectively. The phytosterols stigmasterol, campesterol, and β-sitosterol have been reported in various combinations and concentrations in plants. Prior studies on the unicellular, photosynthetic alga Chlamydomonas reinhardtii have reported a combination of both a phytosterol and ergosterol as sterol components within its cellular membranes; their production has been proposed to use the classical phytosterol biosynthetic pathway. Belonging to the same phylum as C. reinhardtii, our research goal was to identify and characterize the sterol genes and sterol biosynthetic pathway in the genus Chlorella. Through the use of gene gazing, targeted inhibition of the sterol biosynthetic pathway with sterol biosynthesis inhibitors (SBIs) – statin, terbinafine, and azoles – and GC/MS analysis, we identified ergosterol as the major sterol in C. variabilis cell membranes. Moreover, we describe a hybrid ergosterol biosynthetic pathway that is unique to this unicellular, photosynthetic alga. C. variabilis uses the photosynthetic, non-mevalonate, sterol precursor pathway to form isopentenyl
Molecular cloning and characterization of a group 3 LEA gene from Agropyron mongolicum Keng

Late embryogenesis-abundant (LEA) protein is one of the components involved in desiccation tolerance (DT) by maintaining cellular structures in the dry state. In this study, a member of the group 3 LEA, MwLEA1, was cloned from Mongolian wheatgrass ( Agropyron mongolium Keng) based on a homologous sequence from wheat ( Triticum aestivum L .). Its full-length cDNA sequence was 705 bp, encoding a protein of 187 amino acids. The amino acid sequence comparison revealed its high homology with LEA proteins from other plant species. The deduced MwLEA1 protein had five repeat 11- amino-acid motifs, with a molecular weight of 19.4 kDa and a theoretical isoelectric point of 8.8. Subcellular localization indicated that the MwLEA1 was localized in the nucleus of the onion epithelial cell. Under water stress conditions, MwLEA1 exhibited different expression levels, which was higher in root and shoot but lowest in leaf. The expression profiling under different stresses indicated that MwLEA1 played roles in responses to water, salt stresses as well as abscisic acid (ABA) regulation. The gene of MwLEA1 was transformed into tobaccos by Agrobacterium tumefaciens -mediated method. Eleven regenerated plants were analyzed by polymerase chain reaction (PCR) and southern blotting, and 6 of them were proved to be transgenic plants. Key words: Agropyron mongolium Keng, cloning, late embryogenesis abundant, subcellular localization, expression, transformation.
Elaphoglossum nidusoides (Dryopteridaceae), a New Species of Fern from Madagascar with an Unusual Phylogenetic Position in the Squamipedia Group

Abstract A fern from Madagascar is described and illustrated as a new species, Elaphoglossum nidusoides. We investigated its phylogenetic relationships within Elaphoglossum based on analyses of three non-coding plastid loci (trnL-trnF, rps4-trnS, atpB-rbcL) in 30 species representative of the diversity of the sections in the genus. Our results show that E. nidusoides belongs to section Squamipedia. This is an unexpected phylogenetic position because the new species has a short-creeping rhizome, phyllopodia, fronds glabrous or nearly so and more than 15 cm long, and lacks the characteristic peg-like aerophores on the rhizome. Nevertheless, its position as sister to another Malagasy species, E. marojejyense, is supported by the succulent fronds.
AMMONIA, Na+, K+ AND Cl- LEVELS IN RAINBOW TROUT YOLK-SAC FRY IN RESPONSE TO EXTERNAL AMMONIA

Body ammonia content of rainbow trout alevins was about 0.6 micromole g-1 but increased to 4 micromole g-1 after 24 h of exposure to an external ammonia concentration of 36.2 micromolar NH3 (15.8 mmol l-1 ammonia) at pH 7 and 10°C. During ammonia loading, the mass of alevins remained unchanged, but body ion concentrations decreased by about 28 % for Na+ and Cl- and by 35 % for K+. These effects were reduced at lower ammonia concentrations. Exposure for 24 h to 36.2 micromolar NH3 (15.8 mmol l-1 ammonia) at pH 7 and 10°C resulted in a build up of body ammonia that was almost complete within 10 h, whereas Na+ loss from the body was delayed and commenced after about 5 h of exposure. After exposure, ammonia unloading from the body was complete in about 10 h but there was a delay of about 5 h before Na+ uptake commenced. During ammonia exposure, alevins lost substantial amounts of K+ (14 micromole g-1) that were not replaced for several days after exposure to ammonia. Ammonia exposure has major effects on ionic regulation in juvenile fish and possible regulatory processes are discussed.
Molecular Characterization and Identification of Acrostalagmus luteoalbus from Saffron in Iran

Fungi Verticillium Nectria ITS1 ITS4 Several soil samples were collected from saffron fields of the South Khorasan province in the east of Iran during 2012-2014. Fungal isolates with the pale reddish colony, verticilliod conidiophores and hyalospore conidia on rounded pale reddish brown slimy heads were obtained from soil samples. Based on morphological and physiological characteristics, this isolates could be distinguished Acrostalagmus luteoalbus species. The ITS regions of the ribosomal RNA gene were amplified by ITS1 and ITS4 primers and in comparison with GenBank sequences demonstrated more than 99% similarity with A. luteoalbus ITS sequences. This is the first isolation of A. luteoalbus species from mycoflor of the saffron plants in the world.
Comparison of Methods for Determining Coliform and Escherichia coli Levels in Apple Cider †.

The main objective of this research was to determine the easiest and most reliable media for enumerating coliform bacteria and Escherichia coli levels in apple cider. During the autumn of 1994 a total of 59 apple cider samples were collected directly from 12 cider producers and were assessed for bacterial levels and pH. Plate count agar was used to determine heterotrophic bacteria levels. Coliform levels were determined using three different media: violet red bile agar (VRBA), Petrifilm High Sensitivity Coliform Count Plates (PHSCCP), and Trypticase soy agar with a VRBA overlay (TSA/VRBA) for attempted recovery of coliforms injured by the low pH of the apple cider. Eosin methylene blue agar (EMBA) and Petrifilm E. coli Count Plates were used to screen cider samples for E. coli . Apple cider had an average pH of 3.34 ± 0.08. Heterotrophic bacterial levels ranged from 2.30 to 7.11 log CFU/ml. All cider samples contained coliform bacteria with levels varying greatly; on the different media, we found the following: on VRBA, <1.00 to 4.37 log CFU/ml; on TSA/VRBA, 1.20 to 4.40 log CFU/ml; and on PHSCCP, < 1.00 to 4.56 log CFU/ml. Coliform levels were most easily determined in apple cider by using PHSCCP. However TSA/VRBA proved to be more reliable; coliform detection was significantly (P < 0.05) increased. EMBA was ineffective for screening apple cider for E. coli , with the low pH of the cider producing many false-positive results. E. coli was only recovered by using Petrifilm E. coli Count Plates with one of the 59 samples positive for E. coli (non-O157:H7) at a level of 10 CFU/ml.
A Comparison of Attractants Used for Carnivore Track Surveys

Scent-station surveys have been used to examine trends in felid and canid abundance throughout the Southeast. Scent station methods have been developed on the presumption that canids rely on olfactory stimuli and that bobcats (Lynx rufus) rely on sight and auditory stimuli. No studies have quantified the effects of various olfactory, auditory, and visual stimuli on scent-station visitation by bobcats and canids; however, such information could improve the effectiveness and ability of scent-station surveys. We established scent stations and track transects in intensively managed pine forests in east-central Mississippi from August 1989-May 1991 to evaluate the effectiveness of 4 attractants for eliciting response from 3 carnivores. We randomly allocated synthetic fatty acid scent, bobcat urine, an auditory stimulus, a visual stimulus, and a control to stations at monthly intervals. Greatest bobcat visitation rates occurred at stations with audio attractants, whereas greatest coyote (Canis latrans) visitation rates occurred at stations with fatty acid scent and bobcat urine. Gray fox (Urocyon cinereoargenteus) visitation rates were equally great at stations with fatty acid scent, bobcat urine, or audio attractants. An extremely low number of visits by bobcats in our study suggests that more sensitive techniques may be required to adequately index trends in bobcat relative abundance. Fatty acid scent and bobcat urine appeared to elicit greatest responses from coyotes and gray fox. Additionally, our data indicated that transects may be an alterna- tive method to index bobcat, coyote, and gray fox populations relative to scent stations.
Contrasts between marine and freshwater bacterial community composition: Analyses of communities in Lake George and six other Adirondack lakes

The bacterial communities of seven freshwater lakes in the Adirondack Mountains of New York state were examined using culture‐independent methods. β‐Proteobacteria 16S rRNA sequences were recovered from all seven lakes and their presence was confirmed by direct DNA hybridization The results are consistent with phylogenetic and in situ hybridization‐based studies in other freshwater environments, but are significantly different than the results of marine oceanic studies, where β‐Proteobacteria are noticeably absent. This relationship between evolutionary history and environmental distribution is striking, since these phylogenetic clades have not been correlated with consistent physiological features or biochemical capabilities, and there is no a priori reason to expect differences in phylogenetic composition between the environments. In contrast, freshwater relatives to marine phylogenetic clusters, in particular the SAR 11 cluster of the α‐Proteobacteria, were identified. The data imply an underlying physiological distinction between the β‐ and other Proteobacteria groups and potentially an important difference between the composition of bacterial communities in marine and freshwater environments.
An efficient shoot regeneration system for medicinally important Elephantopus scaber Linn.

NAA. On this medium, 98% of the cultures responded, with an average number of 33.7 shoots per explant. The highest frequency of rooting (100%) and mean number of roots (3.3 per shoot) were observed when the shoots were transferred to MS medium supplemented with 1.0 mg L -1 IBA. The plantlets raised in vitro were acclimatized and transferred to soil with a 92% success rate. The protocol described here may be utilized for multiplication and conservation of elite clones of E. scaber.
Intrastock differences in maturation schedules of Atlantic cod, Gadus morhua

Differences in maturation schedules from three subpopulations of North Sea cod (Gadus morhua) were examined using the demographic probabilistic maturation reaction norm (PMRN) approach. Declines in maturation probability with size and age were evident within the North Sea cod stock, but the magnitude of decline differed among subpopulations. The difference in the rate of decline led to significant spatial differences in recent times. Changes in maturation probability could not be explained by colonization from adjacent regions indicating a local response to conditions. The greatest decline in maturation probability followed the near collapse of regional spawning biomass during the 1980s and 1990s. A new methodology was developed to integrate the effects of temperature and competitive biomass into the estimation of the PMRN. Temperature had a positive effect on maturation probability, but could only partially explain the decreasing trend in PMRN midpoints. Consequently, regional selection for early maturing genotypes provides the most parsimonious explanation for the declines in maturation probability observed. The difference in maturation probability among North Sea cod subpopulations, and the additive contribution of temperature to the estimation of change, underscores the need to account for population structuring and to incorporate temperature as a covariate in future applications of the PMRN.