Miracle-dz/UniFAR-FTUs huggingface dataset:
The timber and energy biomass potential of intensively managed cloned Norway spruce stands

We used ecosystem model simulations to study the timber and energy biomass potential offered by intensively managed cloned Norway spruce stands. More specifically, we analysed how the use of cloned trees compared with non‐cloned trees, together with thinning, nitrogen (N) fertilisation and rotation length (from 60 to 100 years), affects the annual mean production of timber (i.e., saw logs, pulpwood) and energy biomass (i.e., stumps and harvesting residuals in the final felling) and its economic profitability [annual mean of net present value (NPV) with a 2% interest rate]. Furthermore, we employed a life cycle analysis/emission calculation tool to assess the total net CO2 emissions per unit of energy (kg CO2 MW h−1) produced based on energy biomass. We found that both the annual mean production of timber and the NPV increased substantially, regardless of the management regime, if cloned trees with an annual growth increase of up to 30% compared with non‐cloned trees were used in regeneration. In general, the use of a short rotation with N fertilisation clearly increased the annual mean of the NPV. Consequently, the use of cloned trees also clearly increased the annual mean production of energy biomass and decreased the total net CO2 emissions per unit of energy produced based on energy biomass. However, the total annual net CO2 emissions were the lowest if a long rotation was used with N fertilisation. To conclude, the use of cloned trees together with intensive management could potentially be highly beneficial for the cost‐efficient and sustainable production of timber and energy biomass in an integrated way.
Fruit Ripening in Sour Cherry: Changes in Expression of Genes Encoding Expansins and other Cell-wall-modifying Enzymes

A preliminary understanding of developmental processes among divergent species is essential to evaluate the applicability of information from model species to plants of agricultural importance. In tomato (Lycopersicon esculentum Mill.), where the molecular biology associated with fruit ripening has been studied most extensively, tissue softening is due at least in part to the activity of proteins called expansins, in concert with enzymatic activities that modify the pectin and xyloglucan components of the cell wall. We evaluated the potential for the concerted action of expansins and other cell wall-modifying enzymes during ripening in a highly divergent fruit species, sour cherry (Prunus cerasus L.). We identified a family of four expansin genes that was strongly upregulated at the advent of ripening. Activation of these genes was accompanied by strong upregulation of gene(s) encoding potential pectin methylesterases, pectate lyase(s), and xyloglucan endotransglycosylase(s). Initiation of ripening and gene induction were also associated with a rapid decrease in cell wall weight. These results suggest that expansin and several other distinct activities could be involved in ripening- associated cell wall modification in cherries. independently, as a modifier of the cellulose-hemicellulose net- work, and synergistically with pectin (and possibly hemicellu- lose) depolymerizing enzymes. In addition to expansin, pectate lyase (PEL) likely plays a key role in fruit softening, at least in some species, as transgenic strawberries (Fragaria ananassa Duch.) in which a PEL-like gene was suppressed were signifi- cantly firmer (Jimenez-Bermudez et al., 2002). We are studying the molecular basis for tissue softening in sour cherry (P. cerasus L.) fruit. Development of this fruit differs from that of tomato, strawberry, and many other fruit in several fundamental respects. For example, cherry exhibits a well-char- acterized, biphasic growth pattern, with softening and other ripening processes coupled with the beginning of the second growth phase (Tukey, 1935). This is distinctly different from tomato, where softening is initiated only after fruit growth has ceased (Brummell and Harpster, 2001). Cherry is a nonclimacteric fruit, in which ethylene does not seem to have an important role in coordinating ripening processes (Li et al., 1994), and, unlike some other nonclimacteric fruit such as strawberry, it is a true, ovary-derived fruit. Finally, cherry development occurs very rapidly (≈55 d from pollination to fully ripe fruit) in comparison with other tree fruit. Sour cherry is included in the genus Prunus, which includes several other horticulturally important fruit crops. Thus, sour cherry represents a potentially valuable model for the study of fruit tissue softening. The goal of this project was to identify genes encoding expansins and other potential cell-wall- modifying enzymes that may play a key role in fruit softening in sour cherry.
DIGGING MECHANISMS AND SUBSTRATE PREFERENCES OF SHOVEL NOSED LOBSTERS, IBACUS PERONII (DECAPODA: SCYLLARIDAE)

Abstract Digging is a distinct form of locomotion that poses different mechanical problems than other locomotor modes that are commonly used by crustaceans, e.g., walking, swimming. I examined the mechanisms of digging by shovel nosed lobsters (Ibacus peronii), which spend most of the day underneath sand. Ibacus peronii were videotaped while digging. Ibacus peronii use a “wedge” strategy to submerge into sand. An individual penetrates the sand with the walking legs, then extends the abdomen to push sand backwards, then flexes the abdomen while pushing backward with the legs, which slowly drives the body into the sand. This basic sequence repeats for several minutes. Digging often ends with a short series of tailflips. Digging by “wedging” is substantially different from previously described mechanisms in more specialized digging species. When presented with a choice of substrates, I. peronii preferred to dig in sand over shell grit, but individuals showed no preference for different types of sand.
G1957C variation in Core Promoter and Precore/Core regions of Hepatitis B virus isolated from men who have sex with men (MSM) in Surakarta, Central Java, Indonesia

Prasetyo AA, Sariyatun R, Prasetyo AD, Yudistiro I, Sidhajati RA. 2014. G1957C variation in Core Promoter and Precore/Core regions of Hepatitis B virus isolated from men who have sex with men (MSM) in Surakarta, Central Java, Indonesia. Nusantara Bioscience 6: 107-110. Little is known about HBV isolates in Indonesian men who have sex with men (MSM) community. Thus, this study was aimed to analyze the genetic profile of HBV isolated from MSM in Indonesia, particularly in Surakarta, Central Java. A total of 205 blood samples were examined by polymerase chain reaction (PCR) targeting the partial Core Promoter (CP) and Precore/Core (preC/C) regions. Three samples were found positive by PCR. The amplicons were sequenced and subjected to molecular analysis. The genetic profile of all HBV isolated in Indonesia (n= 122) were also included for molecular analysis. All HBV isolated from the MSM were genotype B3. G1957C (C195S) was found in all HBV isolated from the MSM community and subject with sex with man history. Several disease-related mutations were observed among HBV sequences from Indonesia, including T1753C, A1762T, G1764A, A1846T, and G1896A which existed in 7.2% (9/125), 17.6% (22/125), 19.2% (24/125), 16.8% (21/125), and 24.8% (31/125) sequences, respectively; however, none were present in HBV isolated from the MSM. In conclusion, various mutations, including those related to disease, were found in Indonesian HBV isolates. G1957C variation was unique in the HBV isolated from the MSM.
Selection of wild hosts for feeding by passion vine hopper Scolypopa australis (Walker) (Hemiptera Ricaniidae) in the Bay of Plenty

Passion vine hopper, Scolypopa australis (Walker) (Hemiptera: Ricaniidae), a pest of kiwifruit, occurs on a wide range of native and introduced plants that are probably not equally preferred as hosts. Firstinstar nymphs and adults were observed on 69% and 53% respectively, of 42 plant species found at varying frequency in a survey of gullies adjacent to kiwifruit orchards in the Bay of Plenty. In choice tests with four plant species common in gullies, first-instar nymphs and adults preferred the native species mahoe ( Melicytus ramiflorus). Under nochoice conditions, survival from first to late instar was also best on mahoe. Of 10 plant species in a no-choice test, adults survived best and laid most eggs on the native species wineberry ( Aristotelia serrata).
Paracentrotus lividus (Echinodermata: Echinoidea) attachment force and burrowing behavior in rocky shores of SW Portugal*

The rock burrowing sea urchin Paracentrotus lividus is a common wave-swept organism that inhabits intertidal rock pools and shallow subtidal temperate shores. Here we present field data on P. lividus attachment force, burrow shape and test diameter measured in different rocky habitats (intertidal pools, low shore intertidal channels and shallow subtidal shores) and in two study sites with different wave-exposure conditions. These data were then analyzed to look for a pos­sible relationship between the size of sea urchins and their attachment force and burrow shape as well as the influence of wave-exposure and habitat in the measured variables. P. lividus test diameter varied among habitats: urchins were smaller in mid-shore intertidal pools and bigger in shallow subtidal shores. We observed in all studied habitats that attachment force was not correlated with test size, while burrow shape index (BSI) was negatively correlated with test size. Results suggest that the attachment force of large and small urchins was similar, but smaller animals occurred in relatively deeper burrows (higher BSI values). Attachment force was positively correlated with BSI, which indicates that burrows may enhance attachment force of P. lividus living in rocky shores by allowing the use of spines as anchorage points and reducing the urchin area exposed to drag forces. Our results partially support the hypothesis that attachment force and BSI might be influenced by local variation in wave-exposure. Higher values for both attachment strength and BSI were measured in intertidal rock pools, the most wave-exposed habitat considered in this study, suggesting that urchins living in such habitat are more able to resist dislodgment by wave-induced forces since they occupy relatively deeper burrows and thusattach more firmly to the substrate. However, neither attachment force nor BSI were higher in the more exposed shore.
Taxonomy and distribution of caecilian amphibians (Gymnophiona) of Brazilian Amazonia, with a key to their identification

Based on examination of 622 specimens of Gymnophiona, 15 species are recognized for Brazilian Amazonia. Geographical variation in characters is low and is mainly restricted to the number of annuli. One new species is described, Microcaecilia rochai sp. nov. New distribution data and maps for most species are provided. A key to the identification of caecilians of Brazilian Amazonia is presented.
Recycling of spent oil bleaching earth as source of glycerol for the anaerobic production of acetone, butanol, and ethanol with Clostridium diolis and lipolytic Clostridium lundense

A major part of edible oil is subjected to bleaching procedures, primarily with minerals applied as adsorbers. Their recycling is currently done either by regaining the oil via organic solvent extraction or by using the spent bleaching earth (SBE) as additive for animal feed, etc. As a new method, the reutilization of the by‐product SBE for the microbiologic formation of acetone, butanol, and ethanol (ABE) is presented as proof‐of‐concept. The SBE was taken from a palm oil cleaning process. The recycling concept is based on the application of lipolytic clostridia strains. Due to considerably long fermentation times, co‐fermentation with Candida rugosa and enzymatic hydrolyses of the bound oil with a subsequent clostridia fermentation are shown as alternative routes. Anaerobic fermentations under comparison of different clostridia strains were performed with glycerol media, enzymatically hydrolyzed palm oil and SBE. Solutes, side product compositions and productivities were quantified via HPLC. A successful production of ABE solutes from SBE has been done with a yield of 0.15 g butanol per gram of bound glycerol. Thus, the biotechnological recycling of the waste stream is possible in principle. Inhibition of the substrate suspension has been observed. A chromatographic ion‐exchange of substrates increased the biomass concentration.
Factors affecting the evolution of development strategies in parasitoid wasps: the importance of functional constraints and incorporating complexity

Parasitoid wasps have long been considered as model organisms for examining optimal resource allocation to different fitness functions, such as body size and development time. Unlike insect predators, which may need to consume many prey items to attain maturity, parasitoids generally rely on a limited amount of resources that are obtained from a single source (the host). This review discusses a range of ecophysiological constraints that affect host quality and concomitantly the evolution of development strategies in parasitoids. Two macroevolutionary differences in host usage strategies (idiobiosis, koinobiosis) are initially described. Over many years, particular attention has been paid in examining a range of quantitative host attributes such as size, age, or stage, as these affect idiobiont and koinobiont parasitoid development. Parasitoids and their hosts, however, constitute only a small part of an ecological community. Consequently, host quality may be affected by a broad range of factors that may operate over variable spatial and temporal scales. Intimate factors include aggressive competition with other parasitoids and pathogens for access to host resources, whereas less intimate factors include the effects of toxic plant compounds (allelochemicals) on parasitoid performance as mediated through primary and/or secondary hosts. It is suggested that future experiments should increase the levels of trophic complexity as these influence the evolution of life history and development strategies in parasitoids. This includes integration of a suite of direct and indirect mechanisms, including biological processes occurring in different ecological realms, such as above‐ground and below‐ground interactions.
Molecular Composition of The Contractile Apparatus of Skeletal Muscle of Akhal-Teke Horses - According to Age, Gender and Geneteic Background

Skeletal muscle constitutes the largest organ system in the mammalian body and is essential for movement and force generation. Muscle tissue has the unique ability to adapt and remodel with regular exercise. Adaptation of equine contractile apparatus to exercise training with a different character occurs at the structural to the cellular andmolecular levels and depends on age, breed, and sex. In Andalusian and Arabian horses from 3 months to 24 years of age, it was found that the mean cross-sectional area occupied by IIA and IIX fibers was greater in stallions than inmares. Inmuscle ofDutchWarmblood foals from birth to 1 year of age, a significant number of fibers coexpress either developmental and type IIa or cardiac– alpha and type I myosin heavy chain (MyHC) isoforms. Endurance training results in increased mitochondrial density, capillary supply, changes in key metabolic enzymes, and increased maximal oxygen uptake and promotes a transition from type II to type I muscle fiber. In horses, prolonged aerobic exercise training has been shown to induce a further decline in the percentage of type IIx MyHC isoform expression and an increase of type I and IIa MyHC isoform expression. Short-duration, high-intensity exercise training stimulates type IIA and hybrid (IIA/IIX) fibers. Therefore, intensive high-speed trotting facilitates muscle fiber hypertrophy and increases the oxidative capacity of type IIX fibers.
Intra-specific genetic relationship among 20 cultivars from Camellia japonica based on ISSR molecular markers.

Camellia japonica has various ecological,horticultural and economical uses.An approach was established using ISSR(Inter-simple sequence repeat) molecular makers to classify and analyze the intra-specific genetic relationship among twenty cultivars represented from C.japonica,collected in China and abroad.Twenty-one couples of primer sequences which could amplify clearly and reproducible electrophoresis bands were screened from sixty couples of primers.Using these primers,153 discernible DNA fragment were generated with 146(95.4%) being polymorphic,indicating pronounced genetic variation at the cultivars level;the band in fingerprinting were converted into "0" or "1",where "1"and "0" indicated the presence and absence of a band,respectively.Nei's diversity indices(H) ranged from 0.40 to 0.48 and Shannon's information index(I) ranged from 0.57 to 0.67. The gene differentiation coefficients ranged from 0.5 to 0.7 and Nm ranged from 0.2 to 0.5. The genetic similarity coefficients(Hs) among the tested cultivars ranged from 0.50 to 0.74,averaging 0.63. The results showed that the genetic differences among the twenty cultivars were relatively little.Combing the results of flower morphology and UPGMA cluster analysis,we could divide the twenty cultivars into two big groups.There were four cultivars in groupⅠ,which all grows in Zhejiang Province and has red flowers.There were sixteen cultivars in groupⅡ,intra-specific genetic relationship complexity.In addition,the results also showed that ISSR molecular maker was suitable to analyze the intra-specific genetic diversities and genetic relationships of C.japonica.
The Interaction of Phenanthridinium Derivatives with Nucleic Acids

This Dissertation is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Dissertations by an authorized administrator of Loyola eCommons. For more information, please contact ecommons@luc.edu. Stelios Aktipis, for the encouragement and advice that he provided during the course of this work. Thanks are also due to Laszlo Badoni, Kenneth Micetich and Nikos Panayotatos for many hours of helpful discussion.
Genetic signature in mineral nutrition in oil palm (Elaeis guineensis Jacq.): A new panorama for high yielding materials at low fertiliser cost

Significant differences in mineral nutrition have been demonstrated between progenies and main categories at PT Socfindo (Jacquemard et al, 2002). New set of investigation has been conducted based on larger genetic background. It includes 489 progenies observed in 25 genetic trials planted in Aek Loba Timur Project and 63 commercial blocs covering around 3500 hectares dispatched through all PT Socfindo estates. Leaf contents in major elements constitute important genetic signature that allows characterization and individualization of nutritional level of each ALT project families according their genetic background. Observations achieved on commercial blocs confirm the signature of ALT project derived commercial categories. Some large groups show very distinct characteristics in their nutrient levels such as: Low Nitrogen - low Potassium Low Nitrogen - high Potassium High Nitrogen - low Potassium In addition, some high yielding families express specific behaviour linking Calcium to their Chlorine absorption, then limiting Potassium absorption. Relation-ship between all these elements is discussed. Providing of high yielding planting material more frugal in fertilizer input is discussed. This new panorama offered to research and oil palm sector is an added value on the way of sustainable palm oil. (Resume d'auteur)
Sows Seropositive to Lawsonia intracellularis (LI) Influence Performance and LI Seropositivity of their Offspring

Starek, M. , G. Bilkei: Sows Seropositive to Lawsonia intracellularis (LI) Influence Performance and LI Seropositivity of their Offspring.Acta Vet. Brno 2004, 73: 341-345. The aim of the study was to test, if seropositivity to L. intracellularis does decline more rapidly in the offspring of Lawsonia intracellularis(LI) positive gilts than in the offspring of LI negative gilts in units infected with endemic Porcine Proliferative Enteropathy (PPE). In a Croatian pigproduction unit late-pregnant gilts were tested by an indirect immunofluorescence antibody (IFA) serum assay for LI. Twenty IFA-positive and 20 IFA-negative gilts were selected. Their 2-weekold piglets (191 from positive gilts, and 192 from negative gilts) were inoculated intragastrically with pure-culture of LI. These animals were tested until 25 weeks of age for seroprevalence of LI. Blood samples were collected at 5, 10, 15, 20 and 25 weeks of age. Seropositivity in offspring of IFA negative gilts was highest at the age of 5 weeks (85.9%) and declined gradually from week 10 to only 6.3% at week 25. At the same time, the offspring of IFA positive gilts showed lower and faster-decaying seroprevalence: 21.4% at week 5 and 0% at weeks 15, 20, and 25. There was no significant difference in the occurrence of diarrhoea between the offspring of LI seropositive and seronegative gilts. Mortality was significantly ( p < 0.05) higher (20.4%) among offspring of seronegative, compared to 14.1% the offspring of seropositive gilts. Average weight gains were higher (p < 0.05, 741 ± 44g vs. 611 ± 41g⋅d-1) among the offspring of seropositive than among of seronegative gilts. The essence of this report is the observation that seropositivity to LI declines more rapidly in grower/finisher pigs born to LI seropositive gilts than the ones born to LI seronegative gilts in units infected with endemic PPE. Gilts, suckling piglets, seroprevalence, mortality, weight gain
AISLAMIENTO, IDENTIFICACIÓN Y CARACTERIZACIÓN PARCIAL DE LAS PROPIEDADES PROBIÓTICAS DE CEPAS DE Lactobacillus sp. PROCEDENTES DEL TRACTO GASTROINTESTINAL DE POLLOS DE CEBA ISOLATION, IDENTIFICATION AND PARTIAL CHARACTERIZATION OF THE PROBIOTIC PROPERTIES OF Lactobacillus sp. STRAINS OBTAINED FROM T

Abstract Isolation of different strains of Lactobacillus sp. from the gastrointestinal tract (GIT) of broilers was carried out aiming to make a preliminary selection and identification of those strains which could resist the main natural barriers in the digestive flow: acid pH (pH 2) and bile salts (1.5 g L−1 of Ox-biles). As result, 20 strains with probiotic activity potential were obtained from poultry. From those, 6 strains were selected for showing higher growth capacity (between 10.50 and 10.83 Log CFU mL−1) and a better production of lactic acid (between 14830.94 and 16747.38 mg of lactic acid/L). These strains were identified as Lactobacillus salivarius, typical specie of the gastrointestinal ecosystem of birds, capable of surviving to chemical barriers and of multiplying at high rate. Resumen Se realizó el aislamiento de diferentes cepas de Lactobacillus sp. a partir del tracto gastrointestinal (TGI) de pollos de ceba con el objetivo de preseleccionar e identificar aquellas resistentes a las principales barreras naturales del tránsito de la digestión: presencia de pH ácido (pH 2) y de sales biliares (1,5 g L−1 de Ox-Bilis). Como resultado se obtuvieron 20 cepas de origen aviar con actividad probiótica potencial, de las cuales fueron seleccionadas 6 cepas por mostrar mejor capacidad de crecimiento (entre 10,50 y 10,83 Log UFC mL−1) y mayor producción de ácido láctico (entre 14830,94 y 16747,38 mg de ácido láctico/L). Estas cepas se identificaron como Lactobacillus salivarius, una de las especies típicas del ecosistema gastrointestinal de las aves, capaces de sobrevivir ante barreras químicas y de multiplicarse a velocidad elevada. Palabras clave: Probióticos, Lactobacillus sp, aislamiento, pollos de ceba