Miracle-dz/UniFAR-FTUs huggingface dataset:
Abscission research: what we know and what we still need to study

Purpose of the review: Abscission, organ separation, is an integral part of the life of a plant. Natural and artificial regulation of abscission can have substantive effects on crop yield and fruit quality. Here we present a brief overview of what we have learned about abscission in recent years as it relates to what we learned about abscission in previous decades, and also what we still need to study. Findings: It has been nearly 100 years since the discovery that ethylene played a role in abscission and more than 50 years since the discovery that auxin played a role. As more hormones were discovered – cytokinins, gibberellins, abscisic acid and jasmonic acid – each has been demonstrated to have at least some effect on the timing of abscission. Auxin is of particular interest because it plays a role in cell differentiation and competence to abscise as well as initiation and control of cell separation. Synthesis of a protective layer at the site of organ separation is common to most abscission processes but may be regulated separate from cell separation. Study of Arabidopsis floral organ abscission has stimulated many new lines of research including work on the signaling peptide Inflorescence Deficient in Abscission (IDA) and an abscission-specific change in cytoplasmic pH that correlates with the process of cell separation. Also, the finding that several genes associated with formation of organ boundaries in plant meristem are expressed in mature abscission zones may provide clues as to the differentiation of abscission zone cells.
Diel feeding chronology of six fish species in Anchuthengu backwater, Kerala

The study examined diel feeding chronology of six fish species in Anchuthengu backwater, Kerala. Over the 24h period, more or less same items contributed to the diet of Arius arius. Mugil cephalus exhibited substantial diel variation in diet composition, with algae forming the main dietary component in the diurnal diet, and prawns in the crepuscular and nocturnal diets. Algae and rotifers formed the main food items throughout the 24h feeding period in Hyporhamphus xanthopterus. No change was noticed in the diel diet composition in Ambassis commersonii. While Caranx ignobilis showed no diel variation, Gerrus lucidus that feeds on a variety of prey items seemed to exhibit some diel variation in feeding. All the fish examined had diurnal feeding peaks. The results indicate that because of diel variation in diet composition and feeding periodicity for these six species, dietary analysis conducted at only one interval would not provide an accurate representation of the diet of these species.
Environmental gradients and micro‐heterogeneity shape fine‐scale plant community assembly on coastal dunes

Questions How do fine scale community assembly processes (e.g. environmental filtering, symmetric competition, hierarchical competition, facilitation) vary along a natural stress gradient on coastal sand dunes? How does local environmental heterogeneity affect these processes? Location Mediterranean coastal sand dunes on the coast of central Italy (Montalto Marina, Lazio region) Methods We quantified spatial (co-occurrence) and functional patterns (degree of divergence in the traits of co-occurring species) at a fine scale (0.5m x 0.5m subplots) in herbaceous communities (2m x 2m plots) of coastal habitats along the sea-inland vegetation zonation. We then studied how the fine-scale co-occurrence patterns (aggregation vs. segregation) varied across habitats of the zonation. Finally, we fitted linear models assessing the relationship of the fine-scale functional patterns (convergence vs. divergence) with 1) the average environmental conditions along the sea-inland environmental stress gradient and 2) the environmental heterogeneity within plots. Results Spatial and functional patterns conveyed complementary information. Within community spatial segregation was more common farther from the sea, which suggests the dominance of competitive processes in the least stressed communities. Fine scale convergence or divergence depended for all functional traits on the average environmental conditions of the community along the gradient, suggesting an effect of environmental stress on the prevailing assembly processes. However, it also depended on the environmental heterogeneity within the community, suggesting that micro-abiotic filtering might play a more important role than previously anticipated in determining fine scale community assembly. Conclusions Our results suggest that contrasting assembly processes act simultaneously on community assembly along environmental gradients both as a function of average environmental conditions and of local heterogeneity. Future studies assessing community assembly should therefore avoid neglecting the role of micro-abiotic filtering in shaping functional patterns. Moreover, only by integrating multiple sources of information (trait patterns, spatial patterns and environmental variation) we were able to disentangle fine scale community assembly processes and reinforce our interpretation of community patterns. This article is protected by copyright. All rights reserved.
Establishing reference intervals for haematological and biochemical blood variables in Lika pramenka sheep

________________________________________________________________________________________ SHEK VUGROVEČKI, A. , A. VOJTA, M. ŠIMPRAGA: Establishing reference intervals of haematological and serum biochemical variables in Lika pramenka sheep. Vet. arhiv 87, 487-499, 2017. ABSTRACT Haematological and blood biochemical variables are key elements for routine assessment of animal health status, with implications in animal production and food safety. However, only reliable reference intervals of haematological and biochemical blood variables can provide the basis for accurate interpretation of the obtained blood results. Haematological and biochemical blood values critically dependent on living conditions, region, husbandry, rearing location, and diet. The aim of this study was to determine the reference intervals for selected important and informative haematological and blood biochemical variables for females of the Croatian indigenous sheep breed, Lika pramenka. We used several advanced statistical methods and assessed their applicability for determination of relevant reference intervals under conditions specific to indigenous sheep breeding. The results show that the reference intervals from the available literature are orientational but not adequate for the specific challenges encountered in raising indigenous breeds in their natural habitat. This was illustrated by the large number of clinically healthy animals with blood variable values falling outside the reference intervals given in the sources available previously.
Response surface methodology-based optimization of glucose acylation bio-catalyzed by immobilized lipase

Abstract This paper describes in detail the selection and optimization of immobilized lipases for enhanced regioselective acylation of glucose into glucose monolaurate (GlcML). Initially, nature of biocatalyst, immobilization approach, reaction media, glucose, and lauric acid concentration were screened out. Finally, lipases from Rhizopus arrhizus immobilized on dead mycelia were investigated under various reaction conditions (Temperature, shaking speed, enzyme dose, and water content) following a fully rotatable central composite design (FRCCD) to optimize the activity of lipases. The immobilized lipases-based biocatalysts in the presence of polar solvents (tertiary alcohols) and higher concentrations of substrates i.e. glucose and lauric acid (100 and 300 mmol L−1, respectively) offered conversion rate of 1.5 mmolmin−1 L−1. Moreover, optimization of reaction conditions revealed that 162.5 lipase units/100mL at 31.25 °C, 3% water content, and 105 RPM shaking speed enhanced the conversion rate by 0.5 mmolmin−1 L−1 rendering the reaction more economical. Hence, lipases-based immobilized biocatalysts may provide an intelligent and green choice for commercial scale synthesis of GlcML for food and pharmaceutical industries.
Effects of Phosphorus Fertility on Competition Between Lettuce (Lactuca sativa) and Spiny Amaranth (Amaranthus spinosus)

Field studies were conducted to determine the influence of phosphorus (P) fertility and method of application (banded versus broadcast) on the competitive interaction of lettuce and spiny amaranth. Weed density significantly affected lettuce head weight and spiny amaranth shoot biomass after 5 wk of interference. Weed density and duration of interference had little or no effect on P content of lettuce tissue. Duration of interference did affect P concentration of spiny amaranth; however, weed density did not Spiny amaranth competition reduced lettuce yield, but P was not the limiting factor. Duration of interference and method of P application interactively affected lettuce head weight; however, only duration of interference affected spiny amaranth biomass. Seven wk of interference caused a decrease in lettuce head weight of 20, 8, and 24% when P was broadcast, banded, or not applied, respectively. Banding of P reduced the negative impact of spiny amaranth on lettuce. Although method of P application influenced the interaction between lettuce and spiny amaranth, interspecific competition between the two species probably was not due to competition for P but some other factor.
Diversity analysis and quantification of lactic acid bacteria in traditionally fermented yaks’ milk products from Tibet

ABSTRACT Fermented yaks’ milk is a characteristic fermented dairy product with a rich microflora (especially lactic acid bacteria [LAB]), that has been produced by Tibetan people in China throughout history. Systematic analysis of the LAB composition of fermented yaks’ milk from central Tibet is essential. In the present study, 38 samples of fermented yaks’ milk were collected from three regions in central Tibet. From these, a total of 211 isolates of LAB were generated using traditional pure culture methods. To accurately analyze their biodiversity, 16S rRNA gene sequence analysis and denaturing gradient gel electrophoresis (DGGE) were used. The isolates were identified as belonging to six genera and 22 species/subspecies. Among them, Lactobacillus species predominated (117 isolates) accounting for 55.45% of all isolates. Overall, L. delbrueckii subsp. bulgaricus (60 isolates; 28.43% of the total) was the most commonly isolated species of LAB from fermented yaks’ milk from central Tibet. Seven Lactobacillus species and the Bifidobacterium genus were confirmed by quantitative PCR (q-PCR). The q-PCR results showed that the abundance of these groups in fermented yaks’ milk from central Tibet ranged from 1.12 ± 0.36 log cfu/ml (for L. sakei from Ningzhong) to 7.77 ± 0.84 log cfu/ml (for L. helvetivus from Ningzhong). Lactobacillus acidophilus, L. delbrueckii subsp. bulgaricus, L. fermentum, L. helveticus varied in concentration depending on the region. The results indicated that traditional fermented yaks’ milk from different regions of central Tibet have complex compositions of LAB species. The diversity of LAB might be related to geographical origin.
A new record and molecular characterization of the Green Turtle Chelonia mydas (Testudines, Cheloniidae) in Sicilian coastal waters

A juvenile specimen of the Green Turtle, Chelonia mydas, was recovered in Sicilian coastal waters close to Avola (Syracuse province, south-eastern Sicily, Italy). Before being released, the specimen was measured and inspected for the presence of ingested hooks or other possible harms to its health. A fragment of the mtDNA marker COI was amplified and sequenced in order to provide the first molecular data for the species from the central Mediterranean area. The possible influence of climate change on the occurrence of this thermophilic species in the central Mediterranean area is briefly discussed.
Occurrence and habitat use of Bryde's whales (Balaenoptera edeni) in the Cabo Frio region, South-eastern Brazil

Ninety-six field trips were conducted between summer 2010 and 2012 in order to understand the occurrence and habitat use of Bryde's whale (Balaenoptera edeni) in the Cabo Frio region, South-eastern Brazil. Bryde's whales were present in the study area between November and July, being observed during all seasons, but occur more frequently during the autumn (Nindividuals = 16) and spring (Nindividuals = 13), followed by summer (Nindividuals = 5) and winter (Nindividuals = 2), respectively. Bryde's whales were observed in water depths ranging from 20.1–100 m. Furthermore, during 2240 min of video recordings, the most frequent behaviour observed was foraging (40.2%; 900 min). Travelling comprised 28.1% (630 min) of observations, while in 33.1% (710 min) behaviour could not be determined. Taking into account the pattern of occurrence, the use of deeper bathymetric bins and the frequency observed, the foraging behaviour of Bryde's whales observed in our study seems to be associated to prey dynamics. Our data show that the study area is frequently used for foraging by this species in Brazilian waters.
Leaf architectural studies in some plants

The shape and structure of leaves vary considerably from species to species of plant, depending largely on their adaptation to climate and available light, but also to other factors such as grazing animals, available nutrients, and ecological competition from other plants. For the present investigation 14 different plants were selected from the college campus, 12 different qualitative and quantitative parameters were selected. All plants showed considerable variations.
Anti-melanogenesis and anti-oxidant of Salix pseudo-lasiogyne water extract in α-MSH-induced B16F10 melanoma cells

ABSTRACT The inhibitory effects of Salix pseudo-lasiogyne water extract (SPWE) on melanogenesis were evaluated using intracellular tyrosinase activity and melanin content in B16F10 cells exposed to α-melanocyte-stimulating hormone (α-MSH). Meanwhile, the antioxidative capacity of SPWE was also investigated. SPWE suppressed intracellular tyrosinase activity and decreased the melanin content in B16F10 cells. The results showed that tyrosinase protein expression was suppressed by the SPWE-treated group. SPWE inhibited mRNA and protein expression of microphthalmia-associated transcription factor (MITF), tyrosinase-related protein (TRP)-1, and TRP-2. SPWE inhibited the intracellular reactive oxygen species level in B16F10 cells. SPWE not only demonstrated 1,1-diphenyl-2-picrylhydrazyl stable free radical (DPPH), and 2,2-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS)-free radical scavenging activity but also possessed chelation capacity and ferric ions (Fe3+) reducing power. We concluded that anti-melanogenesis and antioxidant effect of SPWE may result from the down-regulation MITF and tyrosinase expression and the inhibition ROS generation. Overall, SPWE might be a potential candidate substance for whitening agent about pigmentation.
Salmonella enterica multilocus sequence typing and its correlation with serotypes

ABSTRACT Salmonella enterica is a foodborne pathogen of significant public health concern worldwide. In Thailand, S. enterica has also been ranked among the top five most significant bacterial agents of foodborne illnesses by the Ministry of Public Health. Conventionally, biochemical tests and antigen-antibody agglutination have been used to identify and subtype S. enterica, respectively. The objective of this study was to identify the serotypes of 180 S. enterica isolates. Multilocus sequence typing (MLST) was used to deduce the S. enterica serotypes based on sequence type (ST) correlation as shown in the MLST database (http://mlst.warwick.ac.uk/mlst/). Initially, MLST was used to confirm serotypes of 53 previously identified isolates of S. Enteritidis, S. Typhimurium, S. Hadar, S. Virchow, and S. Infantis isolated in Thailand. MLST and serotype correlation confirmed 52 (of 53) known isolates. MLST was performed in 127 S. enterica isolates of unknown serotypes from various sources. Serotypes of all 127 S. enterica isolates were successfully deduced based on STs. With MLST and PCR-based identification, we have shown that the majority of isolates are of monophasic S. Typhimurium (ST34; 43 isolates) and serotype Rissen (ST469; 37 isolates), in agreement with the top serotypes commonly found in Thailand based on the WHO National Salmonella and Shigella Center. We have also confirmed that MLST is a powerful Salmonella subtyping method which could be used not only as a tracking tool for an outbreak investigation at nucleotide level but also as a serotype predictor for making correlations with food safety regulations.
ANTIGLYCATION, ANTIOXIDANT AND ANTIDIABETIC ACTIVITY OF TRADITIONALMEDICINAL PLANT: RUBIA CORDIFOLIA LINN. FOR MANAGEMENT OFHYPERGLYCEMIA

Rubia cordifolia Linn. a flowering plant species from family Rubiaceae is an important medicinal plant. It is known to have anti-diabetic, antiseptic and antistress properties. In the present paper, antiglycation, antioxidant and antidiabetic activities of roots of Rubia cordifolia Linn. were investigated. Anti-AGE (Advance glycation end products) effect of Rubia cordifolia Linn. on glycation of guanosine with glucose and fructose was analyzed. The inhibitory effect of plant extract on glycation and fructation of guanosine in presence of reactive oxygen species (ROS) generated by hydrogen peroxide, was also analyzed. In vitro antioxidant (DPPH, Superoxide anion scavenging activity and Xanthine oxidase) and antidiabetic assays (Alpha amylase and alpha glucosidase) were performed to determine these activities of plant extract. The UV absorbance of the glycation reactions was found to be maximum at 24 hrs. and with consecutive decreased at 48 and 72 hours. Plant extract of Rubia cordifolia Linn. inhibits glycated and fructated guanosine and ROS-modification of glycated and fructated guanosine. From the results, it is concluded that root extract of Rubia cordifolia has significant antiglycation, antioxidant and antidiabetic activities. The study suggests that Rubia cordifolia Linn. is a natural antioxidant, which might be helpful in management of diseases like diabetes.
Investigations on the Oligomerization of Pyolysin, a Cholesterol-Dependent Cytolysin

The bacterial toxin pyolysin (PLO) is a member of the family of Cholesterol-Dependent Cytolysins, which form large, oligomeric pores in cholesterol-containing membranes. The general CDC structure has an elongated shape and consists of four domains rich in β -sheet structure. Upon binding to a membrane, molecules diffuse laterally on the surface and oligomerize to form a pre-pore complex, then insert into the membrane yielding pores of unusually large size, approximately 30 nm in diameter. In this work, the oligomerization properties of PLO were investigated. In particular, the role of the C-terminal domain in the oligomerization process, the effects of a disulphide-tethered mutant on the activity of the wild type toxin, and the poreforming ability of oligomers pre-formed in solution were characterized. Chapter 2 characterizes the functional properties of a recombinant fragment that corresponds to the C-terminal domain 4 of PLO. It is shown that this fragment can form hybrid oligomers with intact PLO toxin molecules, and is also capable of self-oligomerization. The fragment has no haemolytic activity of its own; nevertheless, it can to some degree increase the haemolytic activity of the wild type toxin. In addition, in a mixture domain 4 and wild type interact in such a way as to form unusual shapes on cholesterol crystals that have not been previously observed. Chapter 3 describes the effects of a disulphide bond linking domain 2 to a membraneinserting region of domain 3 on the oligomerization process. The disulphide mutant was not able to oligomerize on its own, and when combined with active PLO toxin, the haemolytic activity of wild type was significantly inhibited. Also, the combination of the disulphidetethered mutant with intact toxin resulted in the formation of hybrid oligomers. This, in turn, caused an increase in incomplete ring formations on cholesterol surfaces which correlate to a reduction in functional pore size, suggesting that insertion of subunits is partially cooperative. The results of the investigation of the pore-forming ability of solution-derived oligomers (SDO) are described in Chapter 4. Here, the fluorescence emission of an environmentallysensitive probe on the SDO after membrane insertion was a fraction of that observed with the monomeric control, which was supported by hydrophobic quenching analyses. This suggests that the formation of SDO may block necessary conformational changes in the intact toxin to allow membrane insertion.
In the Shadow of Trees: Does Eucalyptus Afforestation Reduce Herpetofaunal Diversity in Southern Brazil?

Abstract. Tree cultivation is widely stimulated due to the provision of environmental services by sequestering atmospheric carbon, but forestry is a potential danger to biodiversity, mainly when cultivation replaces originally non-forested landscapes. Due to the rapid expansion of afforestation in grassland ecosystems, we used environmental descriptors and structure of amphibian and reptile communities as a tool to assess the possible effects of forestry on wildlife. We used pitfall traps with drift fences in Eucalyptus afforestation and native grasslands of the Pampa biome from southern Brazil. Amphibians and reptile species richness was lower in afforestation than in native grasslands. Furthermore, the reptile community found in afforestation was a poor subset of the community recorded in native grasslands. Indeed, the structure of communities for both amphibians and reptiles in afforestation was highly dissimilar from the native grasslands, with major environmental descriptors that influenced this difference being related to the structure of undergrowth vegetation, incident light, and sodium concentration in soil. Amphibians and reptiles proved to be an efficient tool to assess the potential impacts effects of afforestation/forestation since the replacement of natural grassland ecosystems by eucalypt afforestation caused detectable negative effects on the diversity of herpetofauna. Biodiversity conservation strategies in non-forest ecosystems are urgently needed and should encompass policies to restrict the expansion of forestry on the remaining native grasslands.
Reversed graph embedding resolves complex single-cell developmental trajectories

Organizing single cells along a developmental trajectory has emerged as a powerful tool for understanding how gene regulation governs cell fate decisions. However, learning the structure of complex single-cell trajectories with two or more branches remains a challenging computational problem. We present Monocle 2, which uses reversed graph embedding to reconstruct single-cell trajectories in a fully unsupervised manner. Monocle 2 learns an explicit principal graph to describe the data, greatly improving the robustness and accuracy of its trajectories compared to other algorithms. Monocle 2 uncovered a new, alternative cell fate in what we previously reported to be a linear trajectory for differentiating myoblasts. We also reconstruct branched trajectories for two studies of blood development, and show that loss of function mutations in key lineage transcription factors diverts cells to alternative branches on the a trajectory. Monocle 2 is thus a powerful tool for analyzing cell fate decisions with single-cell genomics.