Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential effects of farming practice on cuckoo bumblebee communities in relation to their hosts

Bees are important for vital pollination of wild and crop plants, but are in decline worldwide. Intensification of agriculture is a major driver of bee decline. Organic farming practices are designed to limit environmental impacts of agriculture and can increase bee abundance and species diversity. However, studies have been heavily focused towards some guilds of bees, overlooking others. This includes social brood parasites, cuckoo bumblebees, an understudied bee lineage. Little is known about bumblebee host and cuckoo population dynamics, and the effects of farming practice on cuckoo bumblebees have never previously been evaluated. To compare the effects of farming practice (organic vs conventional) on the abundance, species diversity, and community dissimilarity of cuckoo bumblebees and their hosts, we compared host and cuckoo community metrics across ten matched pairs of organic and conventional farms in Yorkshire, UK. As found by many previous studies, host bumblebees were more abundant on organic farms than on conventional farms. Despite this, cuckoo bumblebees were equally abundant on both farm types. Contrary to prediction, community dissimilarity and species diversity were unaffected by farm type for both host and cuckoo communities. Synthesis and applications: Results suggest that cuckoo bumblebee community metrics are not solely driven by host community metrics, and that cuckoos may respond differently from their hosts to differences among farming practices. This could, in turn, indicate that a unified management practice is not sufficient to conserve all bumblebee species.
Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1

One primary objective of synthetic biology is to improve the sustainability of chemical manufacturing. Biological systems can utilize a variety of carbon sources, including waste streams that pose challenges to traditional chemical processing such as lignin biomass, providing opportunity for remediation and valorization of these materials. Success, however, depends on identifying microorganisms that are both metabolically versatile and engineerable. This has been a historic hindrance. Here, we leverage the facile genetics of the metabolically versatile bacterium Acinetobacter baylyi ADP1 to create easy and rapid molecular cloning workflows, a promoter library, ribosomal binding site (RBS) variants, and an unprecedented number of bacterial chromosomal protein expression sites and variants. Moreover, we demonstrate the utility of these tools by examining ADP1’s catabolic repression regulation, creating a strain with improved potential for lignin bioprocessing. Taken together, this work establishes ADP1 as an ideal host for a variety of sustainability and synthetic biology applications.
Response of Potato Plants to Organic, Bio and Mineral Fertilization

Two field experiments were conducted in a loam soil at the private Farm of El-GamaliaDakahlia Governorate, Egypt during the summer seasons of 2014 and 2015 to study the effect of the various combinations among organic manures, bio and mineral fertilization on the production of safe and economic potato tubers spunta cultivar. Twenty-four treatments were arranged in split – split plot design with 3 replicates, which were the simple possible combination between two sources of organic manure [Farmyard manure (FYM) and compost] as main plots, treatments of mineral fertilization (50, 75, and 100% NPK from recommended doses) as sub plots and three sources of bio fertilization (EM, yeast extract and mixture of multi strains) as sub-sub plot. Thus, the total numbers of every experiment were 72 experimental units. The obtained results indicated that;the mean values of, fresh, dry weights of tubers /plant , number of tuber and total yield of potato ton fed as well as cholorophyll content after 70 days in leaves, Nitrite (No2-N), Nitrate (No3-N), reducing sugars percentages, non-reducing sugars percentages and total sugar percentageswere significantly affected due to adding FYM (20 ton fed) and compost (15 ton fed) during both seasons of the experimentation. The highest mean values of traits were recorded with adding compost. As for, the mean values of parameters under study were significantly increased with increasing NPK from 50 up to 75% of the recommended dose during both seasons, then decreased with adding 100%. In the same way the highest significant values of the aforementioned parameters were recorded with spraying plants by mixture of biofertilization(Azotobacterchroccoccum (AZ), Bacillus megatherium (PSB) and Bacillus circulans (KSB)) (2 ml/L.) followed by spraying EM (2 ml/plant). The highest mean values were recorded with 15 ton fed. compost and inoculation with mixture and 75% NPK RD.
The complete chloroplast genome of a widespread ornamental shrub in China, Magnolia figo (Magnoliaceae)

Abstract Plants in Michelia, presented by Magnolia figo DC, are wonderful resources in Magnoliaceae, covering a series of aromatic plants. Despite extensive studies in this family, the M. figo complete chloroplast genome and the taxonomical status based on the whole chloroplast sequences remain unclear. Herein, we report the complete chloroplast genome of M. figo. The chloroplast genome was 160,113 bp in length, with a large single-copy (LSC) region of 88,113 bp and a small single-copy (SSC) region of 18,797 bp, separated by two inverted repeat (protein-coding) regions of 26,602 bp. A total of 135 CDSs were found, including 129 genes, 85 protein-coding mRNAs, 36 tRNA genes, and eight rRNA genes. The overall GC content was 39.3%, and GC percentages range from 34.3% to 43.2% throughout LSC, IRs, and SSC regions. Phylogenetic analysis showed that M. figo is most closely to Michelia odora and displayed a relationship that three Michelia were nested inside Magnolia. This announcement of the complete M. figo cp genome sequence could provide valuable information for further breeding, cp genetic modification, and phylogenetic study in Magnoliaceae.
Manipulation of plant primary metabolism by leaf-mining larvae in the race against leaf senescence

Plants are often considered as suboptimal food for phytophagous insects, requiring them to employ various adaptive mechanisms to overcome food nutritional imbalances. This could include host-plant manipulation and/or symbiotic associations. The extensive reconfiguration of plant primary metabolism upon herbivory, as well as its impact on herbivores, have been largely overlooked, while studies investigating secondary metabolites is extensive. Here, we document how the apple leaf-mining caterpillar Phyllonorycter blancardella, a highly-specialized insect which completes development within a restricted area of a single Malus domestica leaf over successive different larval feeding modes, maintains nutrient-rich green tissues in its feeding area on green and senescent leaves. For this purpose, we quantified a large number of compounds involved in plant primary metabolism: starch, total soluble sugars, five individual sugars, twenty protein-bound amino acids and twenty free amino acids. Plant alteration can be observed not only on senescing (photosynthetically inactive) but also normal (photosynthetically active) leaf tissues of its host-plant to compensate for detrimental environmental variations. Our results show a differential control of the primary metabolism depending on the larva developmental stage, itself correlated to the fluid-feeding and tissue-feeding modes. Our results also suggest that leaf amino acid alterations favor a faster insect development. Finally, chemical scores indicate that the most growth-limiting essential amino acids are also common to other phytophagous insects and large herbivores, suggesting that these limitations are a general consequence of using plants as food source. We discuss the possible mechanisms responsible for these different manipulative capacities, as well as their ecological implications.
Cofactor F420-Dependent Enzymes: An Under-Explored Resource for Asymmetric Redox Biocatalysis

The asymmetric reduction of enoates, imines and ketones are among the most important reactions in biocatalysis. These reactions are routinely conducted using enzymes that use nicotinamide cofactors as reductants. The deazaflavin cofactor F420 also has electrochemical properties that make it suitable as an alternative to nicotinamide cofactors for use in asymmetric reduction reactions. However, cofactor F420-dependent enzymes remain under-explored as a resource for biocatalysis. This review considers the cofactor F420-dependent enzyme families with the greatest potential for the discovery of new biocatalysts: the flavin/deazaflavin-dependent oxidoreductases (FDORs) and the luciferase-like hydride transferases (LLHTs). The characterized F420-dependent reductions that have the potential for adaptation for biocatalysis are discussed, and the enzymes best suited for use in the reduction of oxidized cofactor F420 to allow cofactor recycling in situ are considered. Further discussed are the recent advances in the production of cofactor F420 and its functional analog FO-5′-phosphate, which remains an impediment to the adoption of this family of enzymes for industrial biocatalytic processes. Finally, the prospects for the use of this cofactor and dependent enzymes as a resource for industrial biocatalysis are discussed.
Podosphaera lini (Ascomycota, Erysiphales) revisited and reunited with Oidium lini

Podosphaera lini (Erysiphaceae) has recently been detected on linseed, Linum usitatissimum var. crepitans, in England and represents the first unequivocal record of this powdery mildew species from Great Britain. The history of powdery mildew on linseed/flax in the UK is critically discussed. DNA sequence data (ITS + 28S rDNA) have been retrieved, from the British material and a specimen from Germany, to be used for phylogenetic analyses. The position of P. lini as a species of its own in the genus Podosphaera, close to P. macularis (hop powdery mildew), was confirmed in the ITS-based phylogeny. The phylogenetic results, in concordance with the morphological traits of the flax powdery mildew (small peridial cells of the chasmothecia), place this species in Podosphaera sect. Sphaerotheca subsect. Sphaerotheca. Oidium lini, described from Croatia by Skoric in 1926, was later erroneously reduced to a synonymy with Golovinomyces orontii. Oidium lini has been reassessed and is now regarded as a synonym of Podosphaera lini. Oidium lini, cited in the literature as a name published by Bondartsev in 1913, is critically discussed and reviewed. The name O. lini was most likely never validly introduced and is doubtful.
Nutritive value of enzyme-supplemented carinata meal for growing pigs1

Abstract Carinata meal is increasingly available for livestock feeding. However, the effects of supplemental phytase and fiber degrading enzymes on nutritive value of carinata meal for pigs have not been reported. Objective of the study was to evaluate the standardized ileal digestibility (SID) of amino acid (AA), and digestible energy (DE) and net energy (NE) values of phytase- and fiber-degrading enzymes-supplemented carinata meal for growing pigs. Ten ileal-cannulated pigs (initial body weight = 53.9 ± 4.76 kg) were fed 4 diets in a replicated 4 × 4 Latin square design with two additional columns to give 10 replicates per diet. Diets included a corn-soybean meal (SBM)-based basal diet, basal diet with 25% carinata meal, basal diet with 25% carinata meal plus phytase at 2,000 FTU/kg and multi-carbohydrase at 0.2 g/kg, and in addition a nitrogen-free diet. The multicarbohydrase supplied 4 units of xylanase, 10 units of β-glucanase, and 1,000 units of pectinase per kilogram of diet. The ratio of corn to SBM and soybean oil in carinata meal-containing diets was identical to that in the corn-SBM-based basal diet to allow calculation of AA and energy digestibility of carinata meal by the difference method. On a dry matter basis, carinata meal contained 50.2% crude protein, 0.88% ether extract, 15.37% acid detergent fiber, 1.82% Lys, 0.96% Met, 1.89% Thr, and 0.64% Trp, respectively. The SID of Lys, Met, Thr, and Trp for carinata meal were 51.4%, 82.2%, 65.9%, and 85.9%, respectively. The DE and NE values for carinata meal were 3,427 and 1,828 kcal/kg of dry matter, respectively. Supplementation of a combination of phytase and multicarbohydrase did not affect the apparent ileal digestibility of AA and SID of AA for the corn-SBM-carinata meal-based diet, and for the carinata meal. However, the combination of phytase and multicarbohydrase did improve (P < 0.05) apparent total tract digestibility, and DE and NE values for carinata meal by 9.4%, 9.5%, and 12.4%, respectively. In conclusion, the enzymes used in the current study could be added in carinata meal-based diets for growing pigs to improve the energy value.
Using Essential Oils to Decrease Potato Tubers Sprouting, Rotting and Insect Infestations during Storage at Ambient Temperature

Two storage experiments were carried out at El-Mansoura Horticultural Research Station, Dakahalia Governorate, Egypt, during four months of storage in summer seasons of 2013 and 2014 for studying the effect of seven treatments, i.e,. natural essential oils and selecron on storability and quality of potato tubers and reduction percentages in the infestations potato tubers moth (PTM) under Nawwala condition. These treatments such as ; clove oil, garlic oil, lemonion oil, eucalyptus oil, peppermint oil, basil oil, mixture of these oils and selecron. The obtained results revealed that all storage treatments expect, selecron and control gave different significantly in all studied characters. Using peppermint and clove oils recorded the lowest significant values of sprouting percentage, sprout weight, sprout length and weight of loss percentage in both seasons. The highest values of dry matter %, starch% and vitamin C were recorded with peppermint oil, but the lowest sugar percentage was obtained by using the same treatment during two seasons. Results indicated that the effects of essential oils and selecron under storage in Nawwala conditions on Phthorimaea operculla (Zell.) (PTM), after four months of storage, the tubers infestation in control were (4848.67%), while the mean reduction percentages of infestation ranged between (94.1098.86% and 93.2396.84) during two seasons of 2013/2014 respectively. Peppermint oil, eucalyptus oil, clove oil and mixture oils gave highest mean reduction percentages of infestation such as selecron. Generally, the obtained data indicated that all used oils offered the highest protection. Also, the results in laboratory showed that the effects of oil treatments on larvae PTM recorded significantly variation according to the type of oil and time of exposure which showed fatal action on the larvae of PTM. The efficacy of Peppermint oil, Eucalyptus oil, clover oil and Mixer oils were the best. The percent of mortality ranged between (76.14 and 100%) compared with selecron. Also, all oils were used effected inhibitor action on adults. The inhibition of egg laying and reduction percentages ranged between were (47.54 %and 95.02 %) of peppermint oil and galaric oils, respectively. This study recommends that it can be sprayed peppermint oil concentration at (2 cm 3 / L / ton) three times during the storage of potato tubers in Nawwala for (4 months) in order to reduce the proportion of sprouting and weight loss and rotting and get a higher percentage of dry matter, starch and less injuries Pferashh (PTM) in tubers. Finally, it could be recommended with peppermint oil, eucalyptus oil, clove oil and mixer oils were the best during storage to obtain the best characters storage and quality. These natural treatments are very safe and potent in improving storability and greatly decreasing PTM insect infection during storage conditions in Nawwala on potato tubers.
AN UPDATE OF THE GENUS ETLINGERA (ZINGIBERACEAE) IN SULAWESI INCLUDING THE DESCRIPTION OF A NEW SPECIES

ARDIYANI, M. & POULSEN, A. D. 2019. An update of the genus Etlingera (Zingiberaceae) in Sulawesi including the description of a new species. Reinwardtia 18(1): 49–60. — A new species, Etlingera mamasarum A.D.Poulsen & Ardiyani was discovered in Gunung Gandangdewata National Park, West Sulawesi. It is similar to Etlingera flexuosa A.D.Poulsen but differs in having flowers which are shorter than the bracts. It is described, illustrated and DNA barcoded. Three additional species (Etlingera cylindrica A.D.Poulsen, E. grallata A.D.Poulsen, E. spinulosa A. D.Poulsen) were documented in this national park and represent new records for West Sulawesi Province. We also update information on the morphology of E. calobates A.D.Poulsen, correct an error in the typification of Alpinia chrysogynia (K.Schum.) K.Schum. and discuss the distribution of the Achasma Group of Etlingera east of Wallace’s Line.
Expression of genes related to soil flooding tolerance in soybeans

The flooded environment brings about injuries to soybeans that vary depending on the adaptation ability of the genotype. Oxygen deprivation promotes the induction of the expression of genes related to glycolysis and fermentation pathways to maintain energy metabolism and, in addition to reducing-power consuming processes, act in the formation of adaptive structures and the maintenance of the redox status of the plant. The aim of this work was to evaluate the relative expression of genes related to soil flooding response in two contrasting soybean cultivars. Soybean plants of the sensitive (BRS 154) and tolerant (I27) cultivars at the V1 development stage were submitted to the flooding and control conditions (without flooding) for 0, 24, 48, and 96 hours. The relative expression of genes associated with flooding, including enolase (ENO), alcohol dehydrogenase 1 (ADH1), alanine aminotransferase 2 (ALAT2), hemoglobin 1 (GLB1), LOB41 domain-containing protein (LBD41), xyloglucan endotransglycosylase (XETP) and ascorbate peroxidase (APX2), was evaluated by means of RT-qPCR. The relative expression, in general, increased with flooding, especially in the root tissue. Cultivar I27 responded positively as observed by the expression of the maintenance genes of energy metabolism, structural changes and detoxification, suggesting the presence of three tolerance mechanisms in the flooding response.
The Amphibians of the Mitaraka massif, French Guiana

ABSTRACT We undertook a 15-day survey of the amphibian fauna of the Mitaraka massif in southwestern French Guiana during the rainy season. We detected 56 species (12 species detected for the first time), including six only thanks to their calls. Thirteen additional species were previously detected from nearby sites. The total number of species occurring in the area is at least 69 but most of the species associated with temporary ponds remained undetected. Therefore, we assume the amphibian community of the Mitaraka massif could reach at least 75 species, which represents one of the richest amphibian faunas of the Guiana Shield. With at least six species not occurring further north in French Guiana, the amphibian fauna of the Mitaraka massif is notably distinct from the rest of the territory. Seven of the species discovered during the survey are highlighted here either because these new records represent range extensions or because they are putative new species.
Gray Wolf (Canis lupus) recolonization failure: a Minnesota case study

During the past few decades, Gray Wolves (Canis lupus) have recolonized many areas in the United States and Europe. In many other cases, however, although dispersing wolves reached areas with adequate prey, a population failed to recolonize. Herein, we provide a case study detailing how a wolf pack attempted for three years to recolonize an area 55 km from a long-established population and within 25 km of Minneapolis and St. Paul, Minnesota, but failed. The pack produced three litters of pups and at one time included 11–19 members, but it preyed on livestock and dogs and, consequently, was lethally removed. The history of this pack’s attempt to recolonize an area long devoid of wolves exemplifies the issues that have prevented earlier recolonizations in non-wild lands in Minnesota and elsewhere and that promise to do so well into the future.
A new species of the genus Liopeltis Fitzinger, 1843 from Vietnam (Squamata: Colubridae)

ABSTRACT A new species of Liopeltis from central Vietnam is described based on morphological and molecular differences. Liopeltis pallidonuchalis sp. nov. is distinguished from its congeners by a combination of the following characters: one single (or missing) loreal; one single nasal shield; dorsal scales in 15–15-15 rows, all smooth; 1 preocular, 2 postoculars and 1 + 2 temporals; 7 supralabials, of which 3rd and 4th in contact with the eye; 8 infralabials; nasal contacting internasal; prefrontal touching or separated from supralabials; ventral scales 126–138; subcaudal scales 67–73, paired; relative tail length about 0.274–0.301; an uniform bronze body colouration; a thin postocular stripe extending from eye to end of the neck becoming indistinct posteriorly. The new species differs from the morphologically closest species Liopeltis frenata by the lower number of ventrals and subcaudals, by characteristic colouration and significant divergence in cytochrome b mtDNA gene sequences (p = 15.3–15.6%). The new species is currently known from northen and central parts of the Annamite (Truong Son) Mountains, central Vietnam, and was recorded from montane evergreen tropical forests of Kon Tum–Gia Lai Plateau (Gia Lai and Thua Thien–Hue provinces, Da Nang City) at elevations of 950–1010 m asl to karst tropical forests in Quang Binh Province in the north at elevation 150 asl. We suggest the new species should be considered as Vulnerable (VU) following the IUCN’s Red List categories. An updated taxonomic key to the Liopeltis species is provided.
Multi-drug resistance bacteria predict mortality in blood stream infection in a tertiary setting in Tanzania

Background Blood-stream infections (BSI’s) are serious and life-threatening infections associated with high mortality and morbidity. In resource limited settings, there is paucity of data on predictors of outcome in patients with BSI. This study aimed at examining the predictors of mortality in patients with BSI as well as bacteria causing BSI. Methods and Materials This was cross-sectional study conducted in Muhimbili National Hospital between April and May 2018. Blood culture results from all inpatients at clinical microbiology laboratory were recorded and clinical information were retrieved retrospectively from the files. Bacteria from positive blood culture were identified and antimicrobial susceptibility was performed. Results The overall prevalence of BSI was 11.4% (46/402), with case fatality rate of 37%. There was significant high rate of BSI in patient who had died compared to those survived p= 0.008. Gram-negative bacteria (74%) were the common cause of BSI, with predominance of Enterobacteriaceae (22), followed by Pseudomonas aeruginosa (11). Majority (70.5%) of the bacteria isolated from patients with BSI were multi-drug resistant. Forty six percent of Pseudomonas aeruginosa were resistance to meropenem. Sixty eight percent 68.2% (15/22) of Enterobacteriaceae were ESBL producers. Carbapenemases production were detected in 27% (3/11) of Pseudomonas aeruginosa and in one Proteus mirabillis. Forty percent (40%) of Staphylococcus aureus were methicillin resistant Staphylococcus aureus (MRSA). Positive blood culture (cOR 7.4, 95%CI 1.24 – 43.83, p 0.03) and admission in ICU cOR 4 (95%CI 1.7 – 9.41, p 0.001) were independent factors for mortality in suspected BSI. Isolation of Multi-drug resistant bacteria was independent predictor for mortality in confirmed BSI (cOR 7.4, 95%CI 1.24 – 43.83, p 0.03). Conclusion The prevalence of BSI was 11.4%, with majority of bacteria in BSI were MDR. Positive blood culture and MDR were predictors for mortality.