Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny of Gardenieae (Rubiaceae) based on chloroplast DNA sequences from the rps16 intron and trnL(UAA)‐F(GAA) intergenic spacer

Chloroplast DNA (cpDNA) sequences of the rps16 intron and the trnL (UAA)-F(GAA) intergenic spacer were obtained from 59 species, to evaluate phylogenetic relationships among members of the Gardenieae, Rubiaceae. The results indicate that Gardenieae is polyphyletic and that genera included in the subtribe Diplosporinae should be transferred to the Coffeeae and Octotropideae. The Octotropideae tribe may also be polyphyletic. It is also demonstrated that the tribe Pavetteae is polyphyletic. In addition, the present data support a basal position for the disputed genus Bertiera within the Coffeeae clade. Of the informal groups proposed by Robbrecht & Puff within the Gardenieae, the Alibertia group is strongly supported, and is estimated to also include Ibetralia, Genipa aff. williamsii, and one undescribed taxon. However, Genipa americana was not part of this clade suggesting that Genipa is polyphyletic. The Tetrad group is not supported, and character optimisations suggest that pollen released in tetrads may have arisen three times. Most of these genera appear in the same clade as the three neotropical genera Sphinctanthus, Rosenbergiodendron, and Tocoyena, all of which bear pollen in monads. Atractogyne, Mitriostigma, and Oxyanthus form the second group with pollen in tetrads, whereas Gardenia is embedded in a third group. Massularia, with polyads, occurs either singly on a large polytomy or at the base of the Atractocarpus-Porterandia-Trukia clade.
Reproductive Demography of Tilefish from the South Atlantic Bight with a Test for the Presence of Protogynous Hermaphroditism

Abstract Length and age at maturity were determined for tilefish Lopholatilus chamaeleonticeps collected off the Georgia coast during the reproductive season. Fifty percent of the females were mature at a total length (TL) of 500 mm and an age of 6 years (the youngest female collected), whereas 50% of males were mature at 450 mm TL and 5 years of age (the youngest male collected); true sizes and ages of median maturity may be less. Fecundity estimates increased nonlinearly with tilefish weight, length, and age and ranged from approximately 0.85 × 106 to 8.5 × 106 eggs for fish ranging from 573 mm TL (2.0 kg, 8 years) to 899 mm TL (8.9 kg, 20 years), respectively. The relationship between fecundity (F) and length was: Log eF = (4.749 logeTL) - 16.508; r2= 0.93; N = 31. We observed disproportionately large numbers of females at smaller lengths and of males at larger lengths. This would be expected if protogynous hermaphroditism were common among tilefish in the South Atlantic Bight. Skewed sex ratios, howev.
Interannual variability in the population dynamics of the main mesozooplankton species in the Gulf of Gdańsk (southern Baltic Sea): Seasonal and spatial distribution*

Abstract The paper characterizes the population dynamics of the major Baltic calanoid copepod species ( Acartia spp., Temora longicornis and Pseudocalanus sp.) in the Gulf of Gdansk (southern Baltic Sea) from January 2006 to December 2007. The data were collected at six stations (M2, S1, S2, S3, S4, J23) located in the western part of the Gulf of Gdansk. The objective of this research was to describe and compare the seasonal and spatial distributions of these three major copepod species. Their distributions in the study area are largely similar, although there are some exceptions regarding Pseudocalanus sp. Copepoda development in the Gulf was at its most intense from May to September, peaking in July. The abundance of these species was the least at the shallowest stations. Based on these results, the weighted mean depth WMD per developmental stage was calculated for Pseudocalanus sp. , Acartia spp. and T. longicornis . The paper also compares the abundance (in indiv. m − 2 ) of the copepodite stages of these species in two regions of the Baltic the abundance of these copepodite stages (∑ CII-CVI)ein the Gulf of Gdansk in 2006 was similar to that in the Gotland Basin in the mid-1990s; in spring/summer 2007, however, their abundances were significantly higher (ca 2–4 times) in the former region.
COI sequencing as tool for the taxonomic attribution of Patella spp. (Gastropoda): the case of morphologically undistinguishable juveniles settled on a Patella ferruginea adult

Patella ferruginea is an endangered marine gastropod, distributed on the western Mediterranean coasts, whose range has progressively contracted, due to intense human exploitation. A genetic analysis was performed on two unidentified young individuals belonging to the genus Patella found attached to the shell of an adult of P. ferruginea, with a twofold aim: (i) to achieve their correct taxonomic attribution by means of the DNA barcoding; and (ii) to shed some light on the hypothesized larval philopatry and/or juveniles phoresis in P. ferruginea. The survey was carried out comparing the sequences of the cytochrome c oxidase subunit I (COI) Folmer region obtained for the two juveniles with those obtained for adults of P. ferruginea, P. caerulea, P. rustica, and P. ulyssiponensis, from different sites of the western Mediterranean, by means of maximum likelihood cluster analysis and a Bayesian-based assignment test. Results obtained evidenced that: (i) COI may be used with confidence as DNA barcoding in the genus Patella; and (ii) the two juveniles studied are not conspecific: one belonged to P. ferruginea, the other to P. rustica. The latter finding raises doubts about the juvenile phoresis and about the occurrence of larval philopatry in P. ferruginea, suggesting that an extensive use of a molecular approach for a better evaluation of the recruitment features of this endangered species should be adopted.
Carbon storage capacity of high altitude Quercus semecarpifolia, forests of Central Himalayan region

Abstract Quercus semecarpifolia, Smith. (brown oak) forests dominate the high altitudes of central Himalaya between 2400 and 2750 m and the timber line areas. The species is viviparous with short seed viability and coincides its germination with monsoon rains in July–August. These forests have large reserves of carbon in their biomass (above and below ground parts) and soil. We monitored the carbon stock and carbon sequestration rates of this oak on two sites subjected to varying level of disturbance between 2004 and 2009. These forests had carbon ranging between 210.26 and 258.02 t ha−1 in their biomass in 2009 and mean carbon sequestration rates between 3.7 and 4.8 t ha−1 yr−1. The litter production in both the sites ranged from 5.63 to 7.25 t ha−1 yr−1. The leaf litter decomposition of species took more than 720 days for approximately 90% decomposition. Even at 1 m soil depth soil organic carbon was close to 1.0%.
Effects of salinity on germination of six salt‐tolerant forage species and their recovery from saline conditions

Abstract Seed germination of six forage species under salt stress and their recovery response from saline conditions were studied. The forage species studied were Bromus inermis, Elytrigia elongata, Puccinellia tenuiflora, Hordeum brevisubulatum, Kalidium gracile, and Suaeda salsa. All of these plants are important forage plants in the inland areas of northern China. Seeds were germinated in solutions of 0, 21, 66, 110, 155, 200, 267, 334, 445 mmol/litre NaCl. After a 21‐day period, the ungerminated seeds were removed to Hoagland solution to observe the recovery germination, radicle, and shoot length. The percentage germination of all the species tested, except E. elongata, significantly decreased with increasing salinity (P < 0.01). The lengths of radicles and shoots were increased at 21 mmol/litre NaCl as compared with that in the control, except for S. salsa. Recovery germination and length of radicles and shoots in Hoagland solution increased with increasing salinity in treatment solutions. The recovery germination performances of the six species indicated that inhibition of germination under NaCl stress was induced by osmotic effects. Shoot growth of P. tenuiflora had the highest tolerance to NaCl stress, which suggests why it is the most widely used plant species for saline soil rehabilitation in northern China. The evaluation of salt tolerance in the early stage of growth should emphasise the response of germination and shoot or radicle growth under salt stress.
Scale formation in an amoeba, Cochliopodium sp.

During excystment of an amoeba, Cochliopodium sp. , scale formation was examined with light and electron microscopy. This amoeba was covered with scales. When the amoeba encysted, the scales remained on the external surface of the cyst wall. Soon after the induction of excystment the Golgi complex began to develop. Many vesicles were extruded from it and changed into vacuoles. Scales were observed first in the vacuole adjacent to the Golgi complex and later in inside the cyst wall. When the amoeba excysted it had been coated by the newly formed scales. It is suggested that the scale formation is dependent on the activity of the Golgi complex.
Tomato inducer of CBF expression 1 (SlICE1) is involved in cold and salt stress signaling.

Aims: Inducer of CBF Expression 1 (ICE1), which is one of basic Helix-Loop-Helix type transcription factors, has important roles in regulation of cold stress-indiced genes of plants. Sample: To investigate functions of tomato ICE1 in cold and salt tolerance, c index (SI), immunochemical assay of endogenous ICE1 protein and RT-PCR of coldinducible genes were conducted with tomato plants. Methodology: Tomato plants grown for 4 weeks were subjected to cold (4oC) and salt (0.2 M NaCl) in the presence or the absence of cell signaling inhibitors. An antibody was raised against ICE1 specific epitoipe. Immunoblot with the anti-ICE1 antibody was carried out with extractions of tomato plants treated by cold and salt stresses. The expression profiles of tomato ICE1 (SlICE1) and other cold-inducible genes including LeCBF1/2/3 and SlTPS1 were analyzed by semi-quantitative RT-PCR. Results: An ICE1-related protein with molecular masses of approximately 55 is induced in tomato plant under chilling and salt stresses. The expression of a tomato ICE1 gene (SlICE1) under chilling stress was maintained at a constant level in contrast to the protein Original Research Article American Journal of Experimental Agriculture, 4(7): 785-796, 2014 786 level. Chilling stress sequentially upregulated tomato CBF homolog, SlCBF1 and trehalose-6-phosphate synthase (SlTPS1). Based on the whole genome database of tomato, cis-elements potentially binding to ICE1 and CBF were located in upstream sequences in promoter regions of SlCBF1 and SlTPS1, respectively. Conclusion: Tomato ICE1 homolog mediates the expression of SlCBF1in a cold-stressinduced transcription factor cascade via binding to ICE1-specific cis-elements, leading to induction of cold tolerance by trehalose synthesis.
The origin and success of polyploids in the boreal circumpolar Flora: A new analysis

Summary Data are summarised that support the secondary contact-balanced hybridity of polyploid evolution in plants. This states that polyploids are most likely to arise and achieve initial success in regions where alternate isolation plus differentiation followed by reunion and hybridisation, in the broadest sense of the word, are most likely to occur. The initial polyploids vary greatly in their evolutionary success. With the passage of time, a small proportion of the original neopolyploids evolve into mesopolyploids, that are widespread, aggressive colonisers, and become abundant over a broad geographical and ecological range. Even later, some of these become diploidised. The resulting paleopolyploids are more like diploids than their original polyploid ancestors with respect to gene pools, geographical distribution and different ecological situations occupied in any region. These conclusions are well supported by a preliminary analysis of polyploidy in the flora of Alaskan Beringia, but more extensive and thorough analyses are needed. Additional data support the hypothesis that chromosome doubling by itself does not adapt plants to withstand severe ecological conditions, such as cold and drought. Finally, high chromosome numbers in some species of angiosperms, plus even higher numbers in a few groups of spore bearing vascular plants, indicate that there is no generally valid ceiling to chromosome numbers. Polyploidisation occurs in cycles. If favourable adjustments of gene dosage occur between cycles, later cycles can include multiplication of base numbers that are already polyploid with reference to the original number of the genus or family.
Emulsification alters simulated gastrointestinal proteolysis of β-casein and β-lactoglobulin

We have studied the effect of the adsorption of milk proteins at the oil-water interface on their digestibility in simulated gastrointestinal environment. The investigations aimed to characterize how both the breakdown of the adsorbed proteins and the interactions with physiological surfactants, phosphatidylcholine (PC) and bile salts (BS), influence structural transformations of model, protein-stabilized food emulsions in the gastrointestinal track. Proteolysis of two contrasting proteins, β-casein (β-Cas) and β-lactoglobulin (β-Lg), was compared between the protein presented in solution or in emulsion, after adsorption at the oil-water interface. Digestion of β-Cas was faster when presented as an emulsion and led to the persistence of a 6 kD peptide not seen when the protein was presented in solution. Adsorption gave rise to a pepsin-susceptible form of β-Lg. Complex interactions were observed with PC introduced to the system in the vesicular form. Measurements of interfacial tension revealed that PC displaced the proteins from the oil droplets after only 30 s for β-Lg and 12 min for β-Cas, so that the gastric digestion largely took place in solution. Pepsinolysis of adsorbed β-Cas played a dominant role in emulsion destabilization. In contrast, collapse of β-Lg-stabilized emulsion under gastric conditions was mainly dependent on protein-PC interactions. β-Lg was significantly protected through simulated duodenal digestion as a result of a complex formed with the PC. In the absence of PC, the proteins were completely broken down after duodenal digestion, during which the duodenal surfactants, BS, displaced any remaining protein from the interface and governed the final structure of emulsion.
Effects of organic manure and chemical fertilizer on soil fertility and productivity of plant and ratoon crops of sugarcane

A study was undertaken to evaluate the effects of integrated use of some organic manures and chemical fertilizers on soil fertility and productivity in plant and the subsequent ratoon crops of sugarcane. The manures included press mud, farmyard manure (FYM) and green manure (Crotalaria juncea) and the fertilizers were urea, TSP, MOP, gypsum and zinc sulphate. Application of organic manure in combination with chemical fertilizer increased absorption of N, P and K in cane leaf tissues both in the plant and ratoon crop as compared with chemical fertilizer alone. This led to higher cane and sugar yield of both crops. The maximum cane yield of 108.4 t ha − 1 and sugar yield of 9.47 t ha − 1 for the plant crop, and 96.8 t ha − 1 cane and 9.18 t ha − 1 sugar yields for the second crop (ratoon) were recorded where FYM at 15 t ha − 1 accompanied with chemical fertilizer (N178P53K54S26Zn2.6 kg ha − 1) were applied. The organic carbon, total N, and available P, K & S contents of soils increased slightly due to incorporation of organic manure. It appeared that 25% reduction of fertilizer application is possible if FYM or press mud at 15 t ha − 1 is used in plant and ratoon crops of sugarcane.
Analysis of soil dwelling rove beetles (Coleoptera: Staphylinidae) in cultivated maize fields containing the Bt toxins, Cry34/35Ab1 and Cry1F×Cry34/35Ab1

In this study, the potential exposure of non-targeted adult rove beetles and their larvae to Bt toxins (Cry34Ab1, Cry35Ab1, Cry1F (59122 and 1507×59122) designed to target western corn rootworm and European corn borer has been determined. The overall assemblage was not significantly affected by the production of stacked proteins.
The stomach (foregut) of the amphipod Bathyporeia sarsi Watkin

Abstract The stomach (foregut) of Bathyporeia sarsi Watkin is described and figured and its functioning explained. A pair of pushers at the stomach entrance delivers the food arriving from the. oesophagus to a central cavity. The hepatopancreatic liquid enters a dorsal cavity; from here it washes through the food contents of the central cavity and drains away through an antero-ventral filter I. A postero-ventral pump (1–2 strokes per sec.) connected to filter I recirculates it to the hepatopancreas through a built-in filter II (porosity 0.9 µ). The circulation is rapid. During feeding, the two hepatopancreatic caeca pump alternately, moving the liquid from the one to the other (maximum frequency 1 cycle per 5 sec.).
Postcranial bones of infant Nacholapithecus: ontogeny and positional behavioral adaptation

We describe the postcranial bones of a partial skeleton of a male infant Nacholapithecus kerioi (KNM-BG 37800) from the Middle Miocene of Kenya. The skeletal elements are associated with dental remains and its age is presumed to be 6–15 months based on a comparison with an infant Proconsul heseloni with a similar dental growth stage. The postcranial elements include the left scapula, a lumbar vertebra, left distal humerus, right proximal ulna, right radius, right and left proximal femora, a proximal fragment of metatarsal, and proximal and intermediate phalanges. Its body mass was estimated as 3.0 kg from shaft dimensions of the humerus and femur. At this early postnatal developmental stage, N. kerioi can be distinguished from P. heseloni in several postcranial features: a caudally projecting lumbar spinous process, strong dorsal divergence of the scapular spine, a coronoid fossa which is more developed than the radial fossa, higher neck shaft angle of the femur, taller trochlea of phalanges, and a lower brachial index. These features, except for the last, agree with the previously proposed positional behavioral reconstruction of N. kerioi, in which vertical climbing, orthograde clambering, transferring, or bridging are relatively important compared with P. heseloni. The apparently low brachial index results from a comparatively short radius for the predicted body mass. This might imply a relatively slow pace of growth in the radius of N. kerioi. However, it might result from body mass overestimation, incorrect length reconstruction, or individual variation. Its interpretation must await further specimens.
Body temperature, size, nuptial colouration and mating success in male Moor Frogs (Rana arvalis)

Variation in colouration has rarely been related to sexual selection in anuran amphibians, even though such a relationship has been proven for many other vertebrate taxa. Male and female Moor Frogs (Rana arvalis )h ave ac ryptic brown colour pattern, but males develop a conspicuous blue nuptial colouration during the reproductive season. To investigate the possibility that colouration plays a role in sexual selection in this species, we studied the temporal variation in blue colouration, determined if body size or body temperature affected blueness and investigated if blueness of males could be related to their mating success. Results confirmed previous observations that males develop and maintain blue colouration for only a very few nights during peak reproductive activity. Colouration of males was unrelated to body size, but males exhibiting higher body temperatures were somewhat bluer than males with lower body temperatures. Further, males in amplexus had higher body temperatures than non-mated males. Finally, mating success was positively related to blueness in small males, whereas in large males no such relationship was detected. While our results align with the hypothesis that the bright blue colouration of males may be a target of sexual selection, alternative explanations are also discussed.
Estimating size and diversity of nitrifying communities in deodorizing filters using PCR and immunofluorescence

An exploration of the characteristics of the nitrifying bacterial community, and more specifically the genus Nitrobacter, colonizing biological filters, was carried out using an immunofluorescence (IF) procedure and the polymerase chain reaction (PCR) together with the most probable number (MPN) technique. The biofilters were made of activated carbon (AC) or peat as the packing material, through which ammonia or industrial gaseous effluents were introduced. Serological diversity amongst Nitrobacter was investigated by the IF procedure. The PCR method was rapid, efficient, and allowed the detection and enumeration of Nitrobacter species in different biological filters on the laboratory and industrial scale. An evaluation of species distribution in this genus was also made in the column. Although the results were promising, it will be necessary to limit DNA and cell losses if the PCR method is to be used for the enumeration of the Nitrobacter population.
Sulfometuron-resistant Amaranthus retroflexus: cross-resistance and molecular basis for resistance to acetolactate synthase-inhibiting herbicides

Summary A biotype of Amaranthus retroflexus L. is the first weed in Israel to develop resistance to acetolactate synthase (ALS)-inhibiting herbicides. The resistant biotype (Su-R) was collected from Ganot, a site that had been treated for more than 3 consecutive years with sulfometuronmethyl + simazine. On the whole-plant basis, the resistance ratio (ED50 Su-R)/(ED50 Su-S) was 6‐127 for sulfonylureas, 4‐63 for imidazolinones, 20‐35 for triazolopyrimidines and 11 for pyrithiobac-sodium. Similar levels of resistance were found also when the herbicides were applied before emergence. Based on a root elongation bioassay, Su-R was 3240-fold more resistant to sulfometuron-methyl than Su-S. In vitro studies have shown that the Su-R biotype was resistant at the enzyme level to all ALS inhibitors tested. The nucleotide sequences of two amplified regions between the Su-S and the Su-R diAered in only one nucleotide. One substitution has occurred in domain A, cytosine by thymine (CCC to CTC) at position 248, that confers an exchange of the amino acid proline in the susceptible to leucine in the Su-R 1 . The proline to leucine change in domain A is the only diAerence in the amino acid primary structure of the regions sequenced, indicating that it is responsible for the ALS-inhibitor resistance observed.