Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of the bacterial cell surface and extracellular macromolecules in U(VI) biosorption and biomineralisation

Uranium biosorption and biomineralisation are processes exhibited by bacteria that aren’t fully understood at a mechanistic level, making it difficult to consider their use and application in remediation, extraction and reuse. The aim of this study was, therefore, to deconstruct the bacterial cell and characterise the specific roles of cell surface structures and extra polymeric substances, in order to elucidate their contribution to the biosorption and biomineralisation of uranium within live cells. The complexation and precipitation of uranium with extracellular DNA (eDNA) was predominantly mediated by negatively charged phosphate moieties within eDNA. The reaction was dependent on pH, where the formation of a precipitate was reduced as the pH increased. Towards circumneutral pH, acid phosphatase liberated phosphate from eDNA that precipitated uranium as a phosphate-bearing mineral. The biosorption of uranium with bacteria is governed by the interactions with functional groups at the cell surface. The cell wall isolates and lysed cells of B. subtilis 168 exhibited a greater uranium retention capacity in comparison to those from P. putida 33015, live cells and cell membrane isolates from both strains. Carboxyl groups and phosphate groups, from proteins and phosphorylated biopolymers, were responsible uranium biosorption with the cell surface structures. The viability and metabolic activity of live cells of P. putida 33015 and D. radiodurans R1 in the presence of uranium was evaluated. An increase in uranium concentration was directly linked to cell toxicity in both strains. At low concentrations of U(VI) and circumneutral pH, viable cells likely sequestered uranium either through biosorption or through the precipitation of enzymatically generated uranium phosphate minerals that were tethered to the cell surface or within EPS as a tolerance mechanism to cope with uranium toxicity. At higher concentrations of uranium or at low pH where the bacterial growth wasn’t favourable or there was cell death, biosorption to the bacterial biomass present likely occurred.
Molecular diversity and distribution of eastern Atlantic and Mediterranean dogfishes Squalus highlight taxonomic issues in the genus

The alpha taxonomy of the globally distributed shark genus Squalus has been under intense investigation recently, and many new species have been described over the last decade. However, taxonomic uncertainty remains about several taxa. Without consistent nomenclature and the ability to reliably distinguish between the different Squalus species, basic data collection, downstream conservation and management efforts are seriously compromised. To aid in clarifying the taxonomic status of Squalus species in the eastern Atlantic and Mediterranean, we assessed species diversity at the molecular level and evaluated the consistency in species identification in the region. Samples from all nominal Squalus species recognized in the above regions were collected in an international effort and sequenced for regions of the mitochondrial COI and ND2 genes. These data were further analysed alongside publicly available sequences, including 19 of the 26 Squalus species globally recognized, to compare the regional genus‐level diversity with that found elsewhere. Our results confirm inconsistent species identification in the eastern Atlantic and Mediterranean Squalus, particularly concerning S. blainville and S. megalops, and reinforce the need to revise the status of S. megalops and S. mitsukurii as they may include several distinct species distributed around the world. The status of S. blainville is also discussed in the light of the current findings and its problematic taxonomic history.
Fatty acid and sterol composition from seeds of some Lathyrus ecotypes

Fatty acids (FA) and sterol distribution in the Lathyrus sativus L. (chickling vetch) and Lathyrus cicera L. (bitter vetch) seeds was determined. The distribution of FA showed that unsaturated (UFA) were predominant to saturated (SFA). In all samples oleic acid predominates between UFA while stearic acid is the most abundant SFA. The sitosterol was the major sterol accompanied by stigmasterol and campesterol
1 patterns in the relative incidence of subterranean termite species infesting buildings in peninsular malaysia

The relative incidence of different termite (Isoptera) species entering buildings in Peninsular Malaysia is reported based on a sample of 81 building infestations, primarily in the vicinity of the capital city. Buildings were broadly categorized as occurring in urban or semi-urban areas based on the density of buildings and existence of vegetation in the area. Termites of the genus Coptotermes accounted for all of the infestations in urban areas and 64% of infestations in semi-urban areas. The Asian Subterranean Termite, Coptotermes gestroi, accounted for 85% of all building infestations in urban areas, while in semi-urban areas, it accounted for 40% of all infestations and 63% of infestations by Coptotermes. It also comprised a large proportion (88%) of a preliminary sample of 17 building infestations from Singapore. Coptotermes kalshoueniand C. curvignathus were found to occasionally infest buildings in Peninsular Malaysia, but the relative incidence of infestations of these species is shown to have decreased over the last two decades, in comparison to the relative incidence of C. gestroi. Two other species of Coptotermes occurring in Peninsular Malaysia, C. sepangensis and C. travians, were not encountered in buildings. Other termites found to infest buildings in Peninsular Malaysia or Singapore were Schedorhinotermes spp. , Globitermes sulphurous, Microcerotermes dubius, Macrotermes giluus. Odontotermes spp. , Microtermes pakistanicus and Nasutitermes spp. Each occurred only rarely in buildings, although together they comprised over a third (36%) of infestations in semi-urban areas in Peninsular Malaysia. The ability of the different termite species to colonize the urban environment and enter buildings is compared. Their points of entry into buildings and the types of wooden structures damaged are discussed.
Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy

Microbes and microbial processes are crucial and quantitatively important players in aquatic environments, and viruses as major agents of microbial mortality and nutrient cycling are a key component of aquatic systems. These roles have led to the need to routinely quantify viral abundance as the part of many investigations. Electron microscopy was first used to demonstrate high viral abundances in aquatic samples; by the mid-1990s, the greater accuracy and higher precision of estimates of viral abundance made by epifluorescence microscopy (EFM) were evident. Initially, DAPI (6-diamidino-2-phenylindole) was the stain used to enumerate virus particles in natural samples, but this dye was soon superseded by a new generation of much brighter fluorochromes. This article outlines detailed protocols for enumerating virus particles in aquatic or sediment samples using SYBR Green, SYBR Gold, and Yo-Pro-1. Each of these stains has advantages and disadvantages, but for natural water samples they produce indistinguishable estimates of viral abundance when the appropriate protocols are
ESTUDIO DE SEGUIMIENTO DEL EFECTO ANTI-GARRAPATA DE LAS LEGUMINOSAS TROPICALES Stylosanthes humilis (L.) Y Stylosanthes hamata (L.) DE UN AÑO DE EDAD

Fern:lndez-l~uvalcaha M, CruzV :izquez C, (;arciaVazquez Z, Santigeral 0.'. Tec Pecu Mex 1999;37 (3)51-56. The value of the tropical legumes . )ty[osanthes humi[is and Sty[osanthes hamata as anti-tick agents was evaluated in plots containing one year old plants experimentally infested with Boophi[us microp[us larvae, using Cenchrus ciliaris as a control. The total nunlhers of live tick larvae recovered hy the douhle flannel flag technique from the experimental plots four weeks after infestation. were 21.9% for S. humilis, 18% for S. hamata and 20.8 for C. ciliaris. Differences were not oh served (P> 0.05) hetween treatments, and . ). humi[is and S. hamata of this age did not provide any anti-tick effect unlike a previous study with younger (93d) plants. The potential u. 'e of these plants as a component of a B. microplu. \' management program should therefore he linlited to young plants. 1. Pegram Rt;, 1'atchell R.J, de Castro . JJ, Chizyuka HGB, Crerck M.J, McCosker PJ, Moran MC, Nigarura G. Tick Control: New concepts. World Anim Rev 1993;(74-75):2-11. 2. George . JE. Naturally acquired immunity a~ an element in strategies for the control of tick~ in livestock. Insect Sci Applic 1992;(13):515-523. 3. Kaaya GP. Non-Chemical agents and factors capable of regulating tick populations in uaturt:: A mini rt:vit:w. Insect Sci Applic 1992;(13):587594. 4. CruzVazquez C, GarciaV:izquez Z, QuinteroMartinez M1'. Avances en la inmunizaci6n contra garrapatas del ganado boviuo. Vet Mex 1995;(26):251-262. 5. Skerman PJ, Cameron Dt;. Lt:gumiuosas Forrajera~ Tropicales. Roma, Italia. Ii'AO. 1991: 422-477. 6. Sutherst RW, Rt:id L.J, Krer RA survey of the ability of tropical legumes in tht: genus Stylosanthes to trap larvae of cattle tick, Boophilu.1' microplus (Ixodidae) . Aus J Exp Agric
Activation ou inhibition testiculaire par la photopériode chez plusieurs espèces de rongeurs sahéliens: première mise en évidence d'une variation circadienne de la photogonadosensibilité

Bruno SICARD, Daniel MAUREL, Jean-Claude GAUTUN et Jean BOISSIN Resume Le protocole experimental des (( creneaux de lumiere n, comportant une fraction principale de 7h30 de lumiere et une photofraction secondaire de Oh30 interrompant a des temps variables une nuit de 16 h 30, a montre chez six sur sept especes de rongeurs saheliens etudiees dans le nord du Burkina Faso (14”20’N-14”50”), l’existence d‘une phase circadienne de photosensibilite du mecanisme central controlant la fonction gonadotrope. Chez Gerbillus nigeriae, Taterillus petteri, Taterillus gracilis, Acomys sp. et Mastomys erythroleucus plusieurs programmes d‘eclairement nocturne ont provoque la stimulation de la secretion de la testosterone alors que chez Arvicanthis niloticus, la lumiere a un effet inhibiteur. Chez la derniere espece etudiee, Mastomys huberti, aucune photosensibilite n’a pu etre mise en evidence. L’etude des relations de phase chez ces rongeurs saheliens, de decembre a mars, entre le cycle circadien de la photosensibilite et les variations de la duree quotidienne de I’eclairement naturel, permet d’envisager un role determinant du photo@riodisme dans la regulation saisonniere de l’activite sexuelle.
Aspects Of The Genesis And Maintenance Of Biological Diversity

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Shoot Apex and Nodes Exposed Above-ground Influenced Growth of Sweet Potato Vine Cuttings

Pot-grown ‘Georgia Jet’ sweet potato [lpomoea batatas (L.) Lam. ] vine cuttings, from which the primary shoot apex was removed, developed vines with fewer secondary laterals, but more tertiary laterals, and greater lengths of both secondary and tertiary laterals than were developed when the primary shoot apex was not removed. With eight nodes exposed aboveground, cuttings without the primary shoot apex developed a greater total length of secondary laterals due to longer internodes and greater total vine length than cuttings with the primary shoot apex. Dry weights of storage roots and lateral vines were increased, but dry weight of the primary vine was reduced from cuttings without the primary shoot apex. With four nodes exposed aboveground under field conditions, cuttings without the primary shoot apex developed fewer secondary laterals, less total vine length, and less yield of jumbo grade roots than those with the shoot apex. With eight nodes exposed aboveground under field conditions, cuttings with the primary shoot apex developed a greater number and length of tertiary laterals than those without the primary shoot apex, but the primary shoot apex did not affect secondary laterals, total vine length, or storage root yield significantly.
True Digestibility of Protein in the Small Intestine and the Hind Gut of Cows Measured with the Mobile Bag Technique using 15N-Labelled Roughage

Abstract Using the mobile bag technique the true small intestinal digestibilities of DM, NDF and N were determined in ten samples of whole plant and straw from pea and barley and ryegrass hay labelled with 15N and harvested at different stages of maturity. The bags were preincubated in a pepsin-HCI solution, unserted into the duodenum of dairy cows and recovered from the terminal ileum or from the faeces. The digestibility in the lower gut was also estimated. The N disappearance was higher in bags recovered from faeces than from the ileum for most of the feeds tested; however differences were significant only in pea and barley straw. The disappearance of Kjeldahl N (NK) underestimated true N digestibility (15N) at both recovery sites. NK digestibility measured using bags recovered from the faeces generally agreed with estimates of 15N digestibility measured using bags recovered from the ileum. It is concluded that the mobile bag technique provides a true measure of intestinal nitrogen digestion.
Alterations in the levels of dehydrogenases in a fresh water fish, Tilapia mossambica (Peters) exposed to arsenite toxicity

Arsenite is an inhibitor of many enzymes of carbohydrate metabolism. Arsenite toxicity especially inhibits the lipoamide dependent dehydrogenases of TCA cycle. The fish when exposed to the sublethal concentration of Sodium Arsenite for a period of 24, 48, 72 and 96 hours showed inhibition of Pyruvate Dehydrogenase, Succinate Dehydrogenase and Malate Dehydrogenase ( P < 0.05) while the Lactate Dehydrogenase activity was increased ( P < 0:05) in some selected tissues of Tilapia mossambica. The inhibition of Dehydrogenases results in accumulation of metabolic intermediates and decreases the formation of acetyl CoA and the accumulation of lactate in liver causes a physiological stress in fish during arsenic toxicity.
CONFLICTING CONCLUSIONS FROM LONG-TERM VERSUS SHORT-TERM STUDIES ON GROWTH AND REPRODUCTION OF A TROPICAL SNAKE

A ten-year (1989-1998) mark-recapture study on long-lived aquatic filesnakes (Ac- rochordus arafurae) challenges conclusions from two earlier short-term (1982-1983 and 1985-1988) studies on the same population. Because of methodological shortcomings and substantial annual variation in most demographic traits in this population, the earlier work (1) underestimated mean growth rates (and thus, overestimated age at maturation) and (2) underestimated the mean fre- quency of reproduction by adult females. Based on our more extensive data, we estimate that most filesnakes mature at about three years of age (versus 5-7 years in earlier studies), and that adult females reproduce (on average) once every 3-4 years (versus 8-10 years in earlier studies). These data support two general conclusions. The first is that long-term studies are necessary before we can accurately characterize the mean values for demographic traits of long-lived organisms in var- iable environments. The second conclusion is that the mean value of a trait may be less important than its variance. Even when we have enough data to quantify "mean" values for traits such as age at maturation or reproductive frequency, few individual females in the population may display those values. Instead, a female's life-history depends upon the conditions that she encounters during her lifetime. Biological insight into the life-histories of organisms in such systems will come from con- sideration of the variance, rather than the mean.
Production and nutrient cycling in mixed plantations of Eucalyptus and Albizia in Hawaii

Experimental plantations of pure Eucalyptus saligna (Sm.), pure Albizia fakataria (L.) Fosberg (a nitrogen-fixing spedes), and five proportions of mixtures of these spedes were examined at age 6 for biomass, production, nutrient cycling in litterfall, and re- source-use effidendes. Biomass was greatest in the 34% Eucalyptus/66% Albizia treat- ment, averaging 174 Mg/ha, compared with 148 Mg/ha in the fertilized pure Eucalyptus treatment and 132 Mg/ha for the pure Albizia treatment. The 34% Eucalyptus/66% Albizia treatment also showed the greatest aboveground net primary production (52 Mg ha -x yr -) and annual increment (39 Mg ha - yr-). The N and P content of above- ground litterfall ranged from 35 and 3.5 kg ha- 1 yr- 1 in pure Eucalyptus to 240 and 9.5 kg ha-1 yr-1 in pure Albizia. Nutrient-use efficiency, deftned as Mg of ANPP/kg of nutrient in fine litterfall, was greater for Eucalyptus (1.1 for N, 13.4 for P) than for A/b/z/a (0.2 for N, 5.7 for P). Light-use efficiency ranged from about 14 kJ/MJ of intercepted light in the pureAlbizia treatment, to 17 kJ/MJ in the pure Eucalyptus treatment, to 18 in the 34% Eucalyptus/66% Albizia treatment. The patterns of productivity across the mixtures resulted from the combination of (1) greater nutrient use efficiency of Eucalyptus, (2) greater nutrient cycling under Albizia, and (3) greater light capture and high use efficiency in mixed stands. FOR. SCl. 38(2):393408. ADDITIONd. KEY WOP, DS. Litterfall, resource-use efficiency, nitrogen, phosphorus, ni- trogen fixation.
Biochemical aspects of desiccation induced viability loss in Myristica malabarica Lam. seeds.

Desiccation sensitivity is the well documented characteristic of recalcitrant seeds (Lin and Chen, 1995; Farrent et al., 1996; Finch-Savage, 1996; Pammenter and Berjack, 1999). Viability loss in recalcitrant seeds is the synergistic effect of a large number of metabolic processes. These include mechanical stresses upon the removal of water which cause structural changes at sub cellular (Drew et al., 2002; Hilhorst et al., 2004) cellular (Kozeko and Troyan, 2000) and tissues levels (Liang and Sun, 2000). Alterations in the membrane structural integrity and function due to desiccation are well documented and reflected by the increased leakage of ions, sugars and proteins (Chaithanya and Naithani, 1994; Finch-Savage et al.,1996). The breakdown of metabolic co-ordination in cells may initiate uncontrolled free radical attack and decrease enzymic and non-enzymic protein protection against such oxidative damages (Leprince et al., 1990, Hendry et al., 1992; Hendry, 1993 Pammenter et al., 1994, Pammenter and Berjack, 1999). An important process of viability loss during desiccation of recalcitrant seeds is the formation of free radicals and highly reactive oxygen species which are synthesised as a result of impaired oxidative metabolism (Chaithanya and Naithani, 1994; Come and Corbineau, 1996; Leprince et al., 1999, Pammenter and Berjack,1999;Greggains et al., 2001). A number of protective enzymes like peroxidase, polyphenol oxidases and super oxide dismutase against the highly reactive free radicals have been reported in recalcitrant seeds (Chaithanya and Naithani, 1994; FinchSavage et al., 1996). Myristica malabarica is an endemic tree of Western Ghats in peninsular India, a major floristic component in Myristica swamps. The riparian climate is suited for the easy germination of the recalcitrant seeds, of Myristica malabarica Anilkumar et al. (2002) reported the desiccation and chilling sensitivity of moderately recalcitrant seeds of this taxon. The present study highlights the effects of desiccation on metabolism, leading to loss of viability. The investigation includes the analysis of moisture content, germinability, measurements of electrical conductivity, lipid peroxiation, reduction of tetrazolium chloride, and assay of scavenging enzymes like peroxidase and polyphenol oxidase during desiccation.
Scophthalmus Rafinesque, 1810: The valid generic name for the turbot, S. maximus (Linnaeus, 1758) [Pleuronectiformes: Scophthalmidae]

Depuis 50 ans, le turbot est denomme dans la litterature soit Scophthalmus maximus (Linnaeus, 1758), soit Psetta maxima (Linnaeus, 1758). Norman (1931) avait montre que le nom valide pour le turbot etait Scophthalmus maximus. Cependant, sa recommandation ne fut jamais universellement appliquee, et aujourd'hui la situation reste confuse avec deux noms generiques en usage pour cette espece. Nous resolvons ici ce probleme par l'analyse de travaux recents (morphologiques, anatomiques, moleculaires et ecologiques) portant sur la systematique des Scophthalmidae. L'ensemble des donnees disponibles amene a considerer que Scophthalmus est le nom de genre valide pour le turbot. Accepter ce nom de genre revient non seulement a vehiculer la meilleure information en terme de relations de parente entre especes, mais aussi a simplifier la nomenclature des Scophthalmidae dans les publications traitant de systematique, d'halieutique, d'aquaculture, d'ecologie, dans les guides pour le grand public et les documents legislatifs. Le present travail renforce les conclusions de Chanet (2003) en apportant des arguments supplementaires.
True autochthony and allochthony in aquatic–terrestrial resource fluxes along a landuse gradient

Freshwater and terrestrial ecosystems are connected via reciprocal cross-boundary resource fluxes, where terrestrially derived (allochthonous) organic matter is a critical energy source to freshwater food webs. Therefore, some proportion of aquatic-to-terrestrial resource fluxes, which consist primarily of emergent aquatic insects, are of allochthonous origin (i.e., recycled terrestrial matter). Landuse activities modify basal resources and consumer community composition in aquatic systems and, thereby, aquatic resource fluxes to terrestrial systems. The origin of aquatic–terrestrial resource fluxes and alterations to them caused by land use should be considered to understand these fluxes better. Resource fluxes at the aquatic–terrestrial interface were measured at 10 streams along a forest-to-agriculture gradient. Autochthony in emergent aquatic insects ranged from 10 to 97%. Hence, aquatic fluxes to terrestrial systems drive the flux of matter of aquatic origin (true aquatic flux) and the recycling of terrestrial matter to the terrestrial environment. Land use indirectly affected autochthony of emergent aquatic insects via changes in water chemistry, high-quality resource availability, and in-stream consumer composition. Chironomidae diet shifts along the landuse gradient strengthened the aquatic flux to the land. For every 10% increase in agricultural land cover, aquatically derived matter deposited on land via emergent Chironomidae increased 0.005 g dry mass m−2 d−1. Plecoptera strengthened the aquatic flux and the recycling of terrestrial matter via changes in abundance across the landuse gradient. Aquatically derived matter deposited on land via emergent Plecoptera increased 0.002 g dry mass m−2 d−1 for every 10% increase in coniferous forest cover. Qualitative changes in resource fluxes across the aquatic–terrestrial interface may be driven indirectly by the influences of land use on diets and composition of emergent aquatic insects.