Miracle-dz/UniFAR-FTUs huggingface dataset:
Gauging the Effect of Honey Bee Pollen Collection on Native Bee Communities

Experimental demonstration of direct exploitative competition between foraging honey bees and native bees in wildlands has proven elusive, due to problems of experimental design, scale, and context‐dependence. We propose a different approach that translates floral resources collected by a honey bee colony into progeny equivalents of an average solitary bee. Such a metric is needed by public land managers confronting migratory beekeeper demands for insecticide‐free, convenient, resource‐rich habitats for summering. We calculate that, from June–August, a strong colony gathers as much pollen as could produce 100,000 progeny of an average solitary bee. Analogous to the animal unit month (AUM) for livestock, a hive unit month (HUM) is therefore 33,000 native bee progeny. By this calculation, a 40‐hive apiary residing on wildlands for 3 months collects the pollen equivalent of four million wild bees. We introduce a rapid assessment metric to gauge stocking of honey bees, and briefly highlight alternative strategies to provide quality pasture for honey bees with minimal impact on native bees.
Isolation and Molecular Characterization of Newcastle Disease Virus Genotype VI from Pigeons in Egypt

A pool of brain sample was collected from three pigeons showing torticollis and whitish green diarrhea in Desouk, Kafr-elshiekh Province, Egypt,during January, 2014. Virus Isolation has been pursued by inoculation of brain homogenate into the allantoic sac of 9 day old specific pathogen free (SPF) embryonated chicken eggs and incubated at 37oC for 4 days. Identification of the isolate was carried out by haemagglutination inhibition test using specific polyclonal antisera against NDV and AIV ( subtype H5 and H9), RT-PCR and confirmed by sequencing. Partial deduced amino acid sequence of the fusion protein at the cleavage site revealed that the isolate possessed the motif 112 K-R-Q-K-R-F117 indicating velogenic entity and phylogenetic analysis showed clustering of the study sequence with other genotype IV F gene sequences available in GenBank.The study indicated that pigeons may play epidemiological role in the introduction of a new NDV genotype VI to commercials chicken.
Genetic analysis of paprika genotypes for dry fruit yield in chilli

Ten genotypes of paprika were evaluated for mean performance, variability parameters and association of characters towards dry fruit yield. Based on mean performance, genotype C-6 (‘U.S.609’) was the best for all characters except number of seed fruit-1, ascorbic acid, oleoresin content, capsaicin and capsanthin content. High estimates of genotypic coefficients of variation for numbers of primary branches, dry fruit yield plant-1, fresh ripe fruit yield plant-1 and fruit length indicated that the major part of variability was due to genetic makeup for these traits. Fruit length, fresh ripe fruit yield plant-1 and dry fruit yield plant-1 had higher genetic advance coupled with high heritability indicates the additive gene action. Among the characters analyzed for association it could be concluded that number of fruit plant-1, fruit length, plant height, days from anthesis to harvest and number of primary branches plant-1 would be appropriate selection parameters for improvement of fresh fruit yield.
Habitat preference of the eastern population of the Short-clawed Lark Certhilauda chuana in the Limpopo province, South Africa

The southern African endemic Short-clawed Lark Certhilauda chuana has two geographically isolated populations. Little is known about the smaller eastern population, which is restricted to the Polokwane Plateau, South Africa. To provide input for a conservation strategy for the eastern population, this study evaluated its habitat preference. Territories previously supporting Short-clawed Lark (1995–2005) were visited in the 2008/09 breeding season. Biophysical habitat parameters were measured at each site to determine the differences between active territories and those no longer active. Active territories had significantly less grass cover, more bare ground, shorter grass, smaller trees and had burned more recently. Bush encroachment and a reduction in the fire frequency were identified as serious threats to the Short-clawed Lark. However, overgrazing and harvesting of wood in rural areas may benefit the species.
Resident areas and migrations of female green turtles nesting at Buck Island Reef National Monument, St. Croix, US Virgin Islands

Satellite tracking studies can reveal much about turtles’ spatial use of breeding areas, migration zones, and foraging sites. We assessed spatial habitat-use patterns of 10 adult female green turtles Chelonia mydas nesting at Buck Island Reef National Monument (BIRNM), US Virgin Islands (USVI; 17° 47.4’ N, 64° 37.2’ W) from 2011 to 2014. Turtles ranged in size from 89.0 to 115.9 cm curved carapace length (CCL) (x− ± SD: 106.8 ± 7.7 cm). The inter-nesting period for all turtles ranged from 31 July to 4 November, and sizes of the 50% core-use areas ranged from 4.2 to 19.0 km2. We observed consistency of inter-nesting habitat-use patterns, with all turtles using near-shore (<1.5 km), shallow waters (<–20 m depth) within approximately 10 km of Buck Island. Seven of the 10 turtles remained locally resident after the nesting season; 5 turtles (50%) established resident foraging areas around Buck Island, 2 established resident foraging areas around the island of St. Croix, and the other 3 (30%) made longer-distance migrations to Antigua, St. Kitts & Nevis, and Venezuela. This is the first empirical dataset showing limited migration and use of ‘local’ resources after the nesting season in the USVI by this unique management unit of green turtles. Five of the turtles had resident foraging area centroids within protected areas; thus, inter-nesting and foraging areas at BIRNM that overlap with human use zones present an important management concern. Delineating spatial areas and identifying temporal periods of nearshore habitat use can be useful for natural resource managers with responsibility for overseeing vulnerable habitats and protecting marine turtle populations.
Anti-inflammatory and analgesic activities of Tephrosia purpurea Linn. aerial and root extracts

An ethanolic extract of the aerial (EETPA) and root parts of Tephrosia purpurea Linn. (EETPR) was investigated for anti-inflammatory and analgesic activities. The extract (250, 500 mg/kg, b.w) produced dose-related inhibition of carrageenan-induced paw edema and cotton pellet-induced granuloma in rats. At the same doses, analgesic activity was also observed by tail immersion method maintained at 55°C. The results of the present study further confirms that the use of Tephrosia purpurea Linn. Traditionally used for the treatment of painful inflammatory pathological conditions like fracture and dislocation.
Long Non-Coding RNAs, Ubiquitin Proteasome System, CollagenDegradation and Preterm Premature Rupture of Membrane

Preterm Premature Rupture of the Fetal Membranes (PPROM) is a reproductive system disorder and a major cause of prematurity. Several major etiologic factors have been linked to PPROM, one of which is the weakness of the amniochorion Extra Cellular Matrix (ECM) caused by collagen degradation. With increasingly deeper research studies on the human genome, rapidly growing evidence has suggested that abnormally expressed non-coding RNAs (ncRNAs) are involved with multiple diseases. Among various ncRNAs, the long non-coding RNAs (lncRNAs) have attracted more attention and were found to correlate with various inflammation-related conditions or diseases. Recent studies demonstrated that lncRNAs might be involved in regulation of the ubiquitin proteasome system (UPS) in PPROM. The UPS is an ATP-dependent enzyme process that targets substrate proteins, tagged with an isopeptide chain composed of covalently linked molecules of ubiquitin, for degradation by the 26S proteasome, and deeply involved in the regulation of most basic cellular processes. Here, we reviewed the UPS system, the collagen in extracellular matrix (ECM), the PPROM as well as lncRNAs. We hypothesize that a novel pathogenic pathway of “infection/inflammation lncRNA, UPS, collagen, membrane rupture” for exploring the molecular pathogenesis of PPROM
European Turtle Dove Streptopelia turtur diet composition in Southern Spain: the role of wild seeds in Mediterranean forest areas

ABSTRACT Capsule: The diet of European Turtle Doves Streptopelia turtur in Mediterranean forest contained a large volume of wild plant seed but from a small number of key species. Aims: To determine which seed species are consumed by Turtle Doves in Mediterranean forest areas. Methods: Digestive tract contents were identified and evaluated for 222 Turtle Doves shot by hunters during three consecutive years. Results: Thirty seed species were identified in the diet, but only a few species represented most of the volume and frequency. Wild plant seeds appeared in 65.8% of digestive tracts and showed significant variation between years. Although the main wild seed species consumed each year varied annually, certain species were found in the diet every year in high volume and frequency. Adults showed a more diverse and numerous consumption of wild seeds than did juveniles. Plastic granules were also found in 3.8% of individuals. Conclusion: A greater number of wild seed species was found in the diet in contrast to previous studies performed in farmland. Echium plantagineum and Amaranthus deflexus could be important seed sources for Turtle Doves in Mediterranean forest. Additionally, the herbaceous species found in the diet whose seeds ripen earlier in the season might play an important role in Turtle Dove reproductive performance, since they are frequently the only available food in the first half of the breeding season.
Trichoderma: A significant fungus for agriculture and environment

The novel technologies in all areas of agriculture have improved agricultural production, but some modern practices affect the environment. The recent challenge faced by advanced farming is to achieve higher yields in environment-friendly manner. Thus, there is an immediate need to find eco-friendly solutions such as wider application of biocontrol agents. Among various types of species being used as biocontrol agents, including fungi and bacteria, fungal genus Trichoderma produces different kinds of enzymes which play a major role in biocontrol activity like degradation of cell wall, tolerance to biotic or abiotic stresses, hyphal growth etc. The understanding of filamentous fungi belonging to the genus Trichoderma has continuously evolved since last two decades, from the simple concepts of biocontrol agents to their recently established role as symbionts with different beneficial effects to the plants. Recent findings from structural and functional genomics approaches suggest the additional use of these microbes as model to study mechanisms involved in multiple player interactions that is, microbes-microbes-plant-environment. In this work, historical development of Trichoderma spp. , mode of action against different biological agents, potential applications and recent mass production techniques are summarized and discussed in detail with updated advances with their application in the agriculture and sustainable environment. Key words: Biocontrol agent, mycoparasitism, induced resistance, endophyte, mass production, bioremediation, bioreactors, agrochemicals
Insect pests of cabbage and cauliflower and their natural enemies in agro ecosystem of Kerala

Pests and natural enemies occurring on cool season vegetable crops, cabbage and cauliflower, grown in hill tracts and the newly cultivated plains of Kerala were studied. Analysis of fauna showed that these crops were attacked by eleven pests. The occurrence of pierid butterfly, Appias lyncida Cramer on cruciferous crops is reported for the first time. Incidence of flea beetle, Phyllotreta chotanica Duv. noted during the seedling stage is the first report from these crops. The key pest affecting the crop grown in plains was the cut worm, Spodptera litura (F.) and in the hilly tracts it was Diamond back moth (DBM) Plutella xylostella (L.). Damage in terms of yield loss by S. litura was 30 per cent in cabbage and cauliflower and that by P. xylostella was 38 per cent to heads and 26 per cent to curds. Two coccinellid predators, Chilomenes sexmaculata (F.) and Coccinella transversalis (F.) and the syrphid, Ischiodon scutellaris (F.) were identified from the colonies of aphid, Lipaphis erysimi (Kaltenbach). One parasitoid, Protapanteles sp. was identified from larvae of Plusia signata (F.).
Genetic diversity in sorghum (Sorghum bicolor L. Moench)

Fifty five accessions from ICRISAT with different geographical origins were grown at Department of Forage Crops, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu during June, 2002 in a randomized complete block design with two replications in order to assess the genetic diversity. Five randomly selected plants from each accession were used to record observation on days to 50 percent flowering, plant height, leaf length, leaf breadth, number of leaves, leaf/stem ratio, Stover yield, grain yield per plant and total soluble solids. Genetic diversity was studied using Mahalanobis’s D 2 statistics and clustering of accessions was done according to Tocher’s method. The analysis of variance showed highly significant differences among the accessions for all the characters studied. The clustering pattern revealed that genetic diversity was not necessarily correlated with geographical origins. Stover yield made the largest contribution to total variability (48.82 percent) followed by total soluble solids (19.53 percent) and days to 50 percent flowering (10.98 percent). Multivariate analysis grouped the accessions in to 21 clusters. Cluster II and V were the largest and consisted of 10 accessions each followed by cluster I (8 accessions) and cluster IV (5 accessions). The largest inter cluster distance were observed between cluster XII and XVIII (73.73) followed by VI and XVIII (71.67) indicating that the crosses between accessions of these different clusters could give heterotic responses and better segregants after hybridization.
A comparison of ITS sequence data and morphology for Calligonum pumilum and C. mongolicum (Polygonaceae) and its taxonomic implications

Several lines of evidence including morphology, chromosome numbers, karyotypes, and phenology were previously used to clarify the taxonomic relationship between Calligonum mongolicum and C. pumilum (Polygonaceae). We employed sequences of the commonly used bar-coding locus, the nuclear ribosomal ITS region, to differentiate Calligonum mongolicum and C. pumilum , based on a sampling scheme of seven populations in three desert regions in China. Phylogenetic analyses did not support the monophyly of each of the two species; instead, populations of the two taxa are intermixed in the analysis. This pattern of intermixing is consistent with the result of the neighbor-net analysis. The ITS region can distinguish other species beyond the C. mongolicum complex defined by morphology both within a section and among sections in Calligonum . The intermixed non-monophyletic pattern of the widespread C. mongolicum and the narrowly distributed C. pumilum supports the merge of C. pumilum with C. mongolicum , consistent with morphological, cytological and karyotype analyses. We herein formally treat C. pumilum as the synonym of C. mongolicum .
Process Optimization of L-Glutaminase Production; a Tumour Inhibitor from Marine Endophytic Isolate Aspergillus sp. ALAA-2000

L-Glutaminases have received significant attention recently owing to their potential applications. All endophytic fungi recovered from the marine soft sponge Aplysina fistularis were able to produce L-glutaminase. During screening program, Aspergillus sp. ALAA-2000 showed the highest L-glutaminase production levels. The production of L-glutaminase by Aspergillus sp. ALAA-2000 was evaluated under different fermentation modes and parameters. The L-glutaminase synthesis was increased their yield after the optimization of fermentation parameters. The hot water 40°C was the best leaching agent extracted of soy bean for L-glutaminase production (21.89 U/ml) under solid state fermentation (SSF). The highest L-glutaminase activity (91.92 U/ml) was achieved after two days incubation period under submerged fermentation (SmF). L-glutamine, dextrose, cysteine and Magnesium chloride supported the highest L-glutaminase production by Aspergillus sp. ALAA-2000 under SmF at pH 4 and 27°C. Single peak of L-glutaminase was obtained from the culture supernatant of Aspergillus sp. ALAA-2000 through ammonium sulfate precipitation and DEAE-cellulose column chromatographyrefer to the mono meric nature of L-glutaminase enzyme. The parameters of purified L-glutaminase were optimized as follow: pH 10, stable at 40°C to 50°C, reaction time 30 min and substrate concentration 4.38 mg/ml. Whereas the maximum activator cation is Na+ and different EDTA concentrations have no effect on L-glutaminase activity which means that L-glutaminase enzymes was represent as a non-metallic enzyme.
Oligomerization and fibrillization properties of amyloid peptides and interactions with inhibitors

Amyloid diseases, including Alzheimer's (AD), Parkinson's, Prion diseases and type 2 diabetes mellitus (T2DM), are characterized by the accumulation of insoluble fibrillar aggregates in tissues. These diseases are the result of the aberrant folding of proteins that constitute the main component of the fibrils. My thesis project focused on two amyloid peptides: β-amyloid peptide, a 40/42 residue peptide involved in AD, and Islet Amyloid PolyPeptide (IAPP), a 37 residue peptide linked with T2DM. Although the mechanism of oligomerization is still unclear, it is known to be a stepwise process that includes a nucleation phase, where the peptides are mainly monomeric and slowly form aggregates, followed by an elongation phase, characterized by the formation of large prefibrillar oligomers leading to mature fibrils. A first part of my project focused on the early stages of fibrillation of IAPP, using a set of complementary biophysical techniques. This study showed that the oligomerization pathway of IAPP involved no or short time lived oligomers favoring the formation of large aggregates. In a second step, I investigated the effect of residue 18 and global charge of IAPP by a mutational analysis of residue His18 and biophysical analysis at pH 5.5 and 7.4. The results showed that (1) the substitution of His18 slowed down the kinetics of fibrillation of IAPP by affecting the interactions between monomers, (2) acidic pH was unfavorable for the process. Finally, we examined the interaction of amyloid peptides with potential inhibitors of synthetic (sugar or fluor-based peptides) or natural origin (epigallocatechingallate). Different mechanisms of action could be characterized.
Variation in Aselliscus stoliczkanus based on morphology and molecular sequence data, with a new record of the genus Aselliscus in China

The taxonomic status of the subspecies of Aselliscus stoliczkanus (Mammalia: Chiroptera: Hipposideridae) in China has yet to reach a consensus. To explore the variation and differentiation among populations of A. stoliczkanus from different regions of China, we conducted a series of bat surveys from 2012 to 2015. We performed multivariate morphological analyses using 16 external and 18 skull measurements and compared the sequence divergences of 2 mitochondrial genes (cytochrome b [Cytb] and cytochrome oxidase I [COI]). There were significant differences in external and skull measurements, particularly in the upper and lower canines, in the specimens from Guangxi compared with those from southwestern Yunnan and Guizhou. Sequence variation of the Cytb and COI genes was 11.0–13.2% and 12.4–14.0%, respectively, which represents differentiation at the species level. The samples from Guangxi were clustered with A. dongbacana from Vietnam in the phylogenetic trees based on COI sequences, and their sequence divergence was less than 3.2%. Based on the morphological and molecular results, we inferred that the samples from Guangxi were A. dongbacana, which represents a new record in China. Skull measurements of A. stoliczkanus from southwestern Yunnan exhibited significant morphological differences compared with those from Anlong County of Guizhou, and the sequence divergences of the Cytb and COI genes were 5.7–6.3% and 6.4–6.7%, respectively. Therefore, A. stoliczkanus from southwestern Yunnan and Anlong County of Guizhou might represent different subspecies. Finally, the phylogenetic analyses and minimal Cytb divergences of 0.2–0.9% indicated that specimens from southwestern and central Yunnan should be considered the same subspecies. Samples from Anlong County of Guizhou, Sichuan, and South Yunnan, with low Cytb divergences of 0.1–0.7%, represent another subspecies. A greater COI gene divergence was found between Libo and Anlong County of Guizhou; thus, the samples from Libo might represent yet another subspecies.
Polychaeta (Annelida) as biological assessment tools for monitoring marine ecosystem health

The effects of marine pollution on polychaetes can be measured at the community level, at the level of individual organism or at a sub-organismal level. To examine community-level responses to pollution, the diversity and abundance of polychaetes were examined at sites impacted by an alumina refinery discharge and compared to reference sites. In the impacted areas, the polychaete assemblage was altered in two different benthic habitats and in hard-substrata habitats, and several polychaete indicator species were recorded. These indicator species will be useful for future impact assessments in this tropical coastal environment and may also be useful in other tropical coastal ecosystems. The effects of marine pollution on polychaetes were also examined at finer ecosystem scales, which required the comparison of individuals of the same species. To ensure that these comparisons were not compromised by the presence of cryptic species, the test polychaete, Ophelina cyprophila, was formally described. This species inhabited a copper- and zinc-polluted harbour and was used to examine changes in its associated bacterial assemblage and gene and protein expression. I examined changes in gene and protein expression in O. cyprophila using transcriptome sequencing, 2-dimensional protein gels and western blotting. Genes and proteins involved in respiration and detoxification were differentially regulated in the copper-impacted harbour. In addition, the copper chaperone, Atox1, was upregulated and may be a valuable and specific biomarker of copper contamination. I also used deep sequencing of 16S rRNA bacterial sequences associated with O. cyprophila and found changes at the impacted site, including increases in the abundance of bacteria from the order Alteromonadales. These changes in the bacteria associated with polychaetes could be a useful and novel indicator of metal pollution. In summary, polychaetes were excellent organisms for the detection of marine pollution in the Australian wet-dry tropics.