Miracle-dz/UniFAR-FTUs huggingface dataset:
Encapsidation of the host RNAs by broad bean mottle virus (BBMV) and cowpea chlorotic mottle virus (CCMV)

ENCAPSIDATION OF THE HOST RNAs BY BROAD BEAN MOTTLE VIRUS (BBMV) AND COWPEA CHLOROTIC MOTTLE VIRUS (CCMV) Nipin Shrestha, M.S. Department of Biological Sciences Northern Illinois University, 2016 Dr. Jozef . J. Bujarski, Advisor Encapsidation of the viral genome into capsid is a highly specific process. Despite the viral RNA specificity, evidence of the host cellular RNA co-encapsidation have been shown in some insect viruses like Flock house virus (FHV) and plant viruses like Cucumber necrotic virus (CNV). This study is dedicated to finding the similar evidence of host RNA encapsidation by the two members, BBMV and CCMV of the Bromovirus family – model virus system. The Next Generation RNA sequencing (NGS RNA-seq) can be implemented to sequence the RNAs encapsidated by the highly purified virions. We mapped and aligned the reads obtained from sequencing to the viral references to filter out the co-encapsidated non-viral reads. These co-encapsidated non-viral reads are then classified into different categories on the basis of their origin from the host plants. BBMV and CCMV co-encapsidated 1.465% and 1.323% of the host RNAs respectively. Majorities of the host RNAs encapsidated are nuclear including ribosomal RNAs (rRNAs) and messenger RNAs (mRNAs). Among the co-encapsidated plant RNAs, 21.228% and 35.220% reads are from transposable elements (TEs) in BBMV and CCMV respectively, which make these virions a potential carrier for the horizontal gene transfer (HGT) in plants. NORTHERN ILLINOIS UNIVERSITY DEKALB, ILLINOIS
Importance of environmental and spatial components for species and trait composition in terrestrial snail communities

Despite the huge diversity of soil animals and their recognized contribution to many ecosystem functions, little is known about the relative importance of factors controlling their abundance and distribution. We examined the relative importance of environmental and spatial factors in explaining the species and functional trait composition of terrestrial snail communities at the level of meta‐communities (spatial extent c. 100 × 100 km) in a heterogeneous, intensively used landscape. We hypothesized that both spatial and environmental factors contribute to the variation in community structure across the landscape, but expected environmental variables describing local habitat conditions to be most important.
Investigation into the human premature ageing disease, Hutchinson Gilford Progeria syndrome, using hTERT immortalised fibroblasts

Hutchinson Gilford Progeria syndrome (HGPS) is a rare premature ageing disease affecting children. 80% of “classic” HGPS patients share the same mutation in the LMNA gene that gives rise to characteristics similar to normal human ageing and they usually die in their teens from heart attacks or strokes. Cells taken from progeria patients have a short replicative lifespan in culture and this has necessitated the generation of immortalised progeria cell lines with unlimited growth potential. Evaluation of one such immortalised cell line has revealed loss of progeria cell characteristics, such as nuclear shape abnormalities, and a reversion to a normal nuclear morphology. We attributed this reversion to an increased rate of breakdown of the mutant protein, progerin, which normally causes the nuclear abnormalities. Identification of this underlying mechanism has potential therapeutic applications for HGPS patients. Based on this finding this study demonstrates the effect of an A type lamin target nanobody conjugated to an E3 Ubiquitin ligase, as the first step to a nanobody therapy for HGPS. The development of TATlamin A and TATprogerin fusion proteins, which are capable of transducing into human cells at a desired concentration, allow for future investigation into progerin dose effects. “Atypical” progeria patients have unknown mutations which cause a similar disease but with more varied degrees of severity. The characterisation of an hTERT immortalised cell line, from an “atypical” patient, led to the observation of a genetic instability phenotype, which, in combination with whole exomes sequencing, has enabled the identification of candidate genes within DNA repair and cell cycle regulation. Future identification of another HGPS gene will increase understanding of premature ageing diseases and of normal human ageing.
Morphological and molecular characterization and phylogenetic position of a new record, Tylenchorhynchus zeae, and some known species of Telotylenchidae Siddiqi, 1960 and Merliniidae Siddiqi, 1971 from Iran

In order to identify the plant-parasitic nematodes associated with Berberis vulgaris, Crocus sativus, and Ziziphus zizyphus, 360 soil samples were collected from the rhizosphere of these plants in the South Khorasan Province of Iran during 2012-2014. Among the identified species, Tylenchorhynchus zeae Sethi and Swarup, 1968 of Telotylenchidae Siddiqi, 1960 is a new record from Iran and the isolate is described and illustrated based on morphological, morphometric, and molecular characteristics. The phylogenetic tree inferred from partial sequences of the 28S rRNA (D2D3 segments) grouped the Iranian isolate with other T. zeae sequences, forming a strongly supported clade (Bayesian posterior probability: 100%). T. zeae is reported here for the first time on Ziziphus zizyphus for Iranian nematofauna. Additional morphological and molecular information is also provided for other species including Amplimerlinius globigerus, Merlinius brevidens, Pratylenchoides alkani, P. ritteri, Scutylenchus rugosus, S. tartuensis, and Trophurus impar from B. vulgaris, C. sativus, and Z. zizyphus in Iran.
The complete chloroplast genome sequence of the medicinal and economic plant woad Isatis indigotica (Brassicaceae)

Abstract Chloroplast (cp) genome sequences provide a valuable source for phylogenetic analysis. It becomes a popular useful tool for population and phylogeny in recently report. Here, the complete chloroplast genome of the Isatis indigotica has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 156,670 bp in size and comprises a pair of inverted repeat (IR) regions of 26,995 bp each, a large single-copy (LSC) region of 84,907 bp and a small single-copy (SSC) region of 17,773 bp. The total GC content is 36.5%, while the corresponding values of the LSC, SSC and IR region are 34.2%, 29.7% and 42.3%, respectively. The chloroplast genome contains 140 genes, including 94 protein-coding genes. The phylogenetic analysis showed a strong sister relationship with Raphanus sativus in Brassicaceae. These findings provide a foundation for further investigation of cp genome evolution in I. indigotica and other higher plants.
Insecticide Resistance in Anopheles gambiae s.l Mosquitoes in Awka, Anambra State, Southeast Nigeria

Long-lasting insecticide nets (LLINs) and indoor residual spraying (IRS) are the main methods used for malaria vector control. However, the success of these methods has been hampered by the development and spread of insecticide resistance in major malaria vectors. The emergence of insecticide resistance in Anopheles mosquitoes in Nigeria has enormous implications for vector control interventions in the country. This study aimed to investigate the insecticide susceptibility levels of wild Anopheles gambiae mosquitoes from Southeast, Nigeria to the four main classes of insecticides used for vector control. Larval mosquitoes were collected from different breeding sites and reared in the insectary. Mosquitoes were identified morphologically and two to five day old adult female mosquitoes were used to conduct WHO susceptibility assays against pyrethroid (0.75% permethrin and 0.05% deltamethrin), organochlorine (4% DDT), organophosphate (0.25% pirimiphos-methyl) and carbamate (0.1% propoxur and 0.1% bendiocarb) insecticides. All mosquitoes collected were identified as members of the Anopheles gambiae s.l. The mosquitoes were completely susceptible to bendiocarb (100% mortality). Resistance to permethrin, pirimiphos-methyland DDT was recorded with percentage mortalities of 26.5%, 17.5% and 1.3% respectively. The KDT 50 recorded were 36.7 minutes (0.1% Bendiocarb), 39.8 minutes (0.1% propoxur), 50.9 minutes (0.05% deltamethrin), 91.4 minutes (0.75% permethrin), 116.3 minutes (0.25% Pirimiphos-Methyl) and 119.1 minutes (4% DDT). The results show that there is very high frequency of insecticide resistance in the study area and calls for a need for insecticide resistance management strategies to be implemented in the area.
Effects of dietary supplement of methionine and lysine on blood parameters and fur quality in blue fox during low-protein feeding

Four groups of blue fox (AlopexLagopus) were fed from weaning to pelting with feed of two different protein levels. The metabolizable energy (ME) from protein amounted to 35/30 % in the control group and to 22/18 % in three low-protein groups during the early and late growthperiod, respectively. One of the low-protein groups received an unsupplemented diet. The second low-protein diet was fortified with methionine, and the third with methionine and lysine to the same level as in the control diet. Hematological values, urea and creatinine were lower in all low-protein groups as compared to the control group. The activities of amino acid metabolizing enzymes ASAT, ALAT and GOT in plasma were lower in the low- protein groups although the relative sizes of the liver and kidneys were greater. The lowered protein content in the feed was sufficient for growth, and only a slight negative effect on fur characteristics was observed. The dietary supplementation of methionine and lysine yielded no improvement in the fur quality or other parameters as compared to the unsupplemented low-protein feed, indicating that there was no deficiency of these amino acids in these low- protein feeds.
Assessment of Resistance in Soybean to Pythium ultimum and Sensitivity of Ohio’s Diverse Pythium species towards Metalaxyl

ii Acknowledgments. v Vita . vi List of Tables . x List of Figures . xiii Chapter 1: Assessment of Resistance in Soybean to Pythium ultimum and Effective Rates of Metalaxyl Towards Ohio’s Diverse Pythium species . 1 Literature Review . 1 Chapter 2: Quantitative Resistance in Elite Soybean Germplasm to Pythium ultimum var. ultimum and Pythium ultimum var. sporangiiferum . 12 Introduction . 12 Materials & Methods:. 15 Pythium Isolates. 15 Inoculum for greenhouse assays. 15 Greenhouse Studies. 16
Individual-based analyses reveal high repeatability in timing and location of reproduction in lake sturgeon (Acipenser fulvescens)

Few studies have quantified the repeatability of reproductive decisions by individuals or assessed their relation- ship with environmental variables over multiple seasons for long-lived iteroparous fish species. Using individual-based data collected for 678 lake sturgeon (Acipenser fulvescens) over 8 consecutive years, we evaluated hypotheses regarding spawn- ing periodicity and repeatability of spawning location, spawning time, and environmental cues associated with spawning. At our study site (Upper Black River, northern Michigan, USA), interspawning interval differed between males (2.3 ± 0.08 years) and females (3.7 ± 0.16 years), but was not significantly related to age. Individual spawning behavior was highly repeatable with respect to spawning time (relative day within the spawning season) for both sexes regardless of size or age, but was less repeatable, though still significant, relative to water temperature, river discharge, and lunar phase. Breeding area was also repeatable, with individuals spawning earlier in the season selecting locations further upstream than those spawning later. Repeatability in spawning times and locations suggest that subpopulation differentiation may develop among different spawning groups, even within small and spatially contiguous areas.
The problems with pooling poop: confronting sampling method biases in wolf (Canis lupus) diet studies

Wolf (Canis lupus L., 1758) diet is commonly estimated via scat analysis. Several researchers have concluded that scat collection method can bias diet estimates, but none of these studies properly accounted for interpack, age class, and temporal variability, all of which could bias diet estimates. We tested whether different scat collection methods yielded different wolf diet estimates after accounting for these other potential biases. We collected scats (n = 2406) monthly from four packs via three scat collection methods (at home sites, at clusters of GPS locations, and opportunistically) in and adjacent to Voyageurs National Park, Minnesota, USA, during April–October 2015. Diet estimates were not affected by scat collection method but did vary temporally, among packs, and by age class. To more accurately estimate wolf population diets, researchers should collect 10–20 adult scats/pack per month from home sites and (or) opportunistically from packs that are representative of the population of interest. D.
Human-grey wolf (Canis lupus Linnaeus, 1758) conflict in Shounther valley, district Neelum, Azad Jammu and Kashmir, Pakistan.

Human-wolf conflict is a major issue in various parts of the world due to predation on livestock. Shounther valley (a sub valley of Neelum valley, AJ&K) harbors pasture-based economy in summer season, thereby livestock predation by “Least Concern” grey wolf (Canis lupus) is creating a serious conflict between farmers and wildlife. Present study is the first attempt in this area that aimed to assess the intensity of the conflict in terms of livestock depredation. Study area was divided in to eight (8) study sites and data were collected for five months (May to September, 2011) during field surveys at each study site. Results revealed that 76 livestock heads were depredated by grey wolf during the study period; the highest depredation was recorded at Bhedian study site (22%) followed by Mali (185) and Dukk (13%). Sheep (67%) were more vulnerable to depredation as compared to goats (26%) and horses (4%). Most depredations (24%) were noted in the age groups of > 2 years and the preferred time of depredation was recorded as 11 pm to 5 am (65%). Open pens provided more chances of depredation (61%) as compared to fenced pens (22%) and pastures (17%). Overall depredation during the study period resulted in a loss of PKR 433,000 to 26 farmers that raised a rage against the wolf and consequently a retaliatory killing of three wolves was reported; one was gunned down, second was poisoned and the third killed by guard dogs. Watch and ward and herding practices are very poor as most of the depredations (61%) occurred in the absence of protection. Conflict is rising day by day and hindering the conservation of grey wolf in the study area. A comprehensive awareness program should be started with the consultation of local influential persons to improve herding practices, better watch and ward conditions, use of frightening devices and to change peoples’ attitude toward the wolf presence in the study area. This base-line study would provide a step toward the conservation efforts of this species in Shounther valley.
Chemical composition and antibacterial activity of extracts and compounds isolated from Citrullus colocynthis (L.) Schrad

The aim of this study was the phytochemical screening of different extracts of leaves and stems prepared with three increasing polarity solvents (n-hexane, ethyl acetate and methanol) of Citrullus colocynthis. Our main goal was to investigate the antibacterial activity of different extracts and compounds isolated from ethyl acetate extract of leaves using the agar disc well-diffusion method. Founded results showed that ethyl acetate extracts of leaves and stems possess potential antibacterial activity compared to other extracts against tested Gram-positive and negative bacterial strains. A bioguided isolation of the ethyl acetate extract obtainded from the leaves led to the identification of Cucurbitacin E and the Gluco-Cucurbitacine E. Moreover, a LC-MS analysis of ethyl acetate leaf extract of C. colocynthis permitted the identification of eight other cucurbitacins. Antibacterial activities of the isolated compounds emphasize the importance of sugar moiety. The most important minimum inhibitory concentrations (MIC) values were obtained for the ethyl acetate extract 0.625 mg/mL against Bacillus cereus and Glucocucurbitacin E 1.25 mg/mL against both Bacillus cereus and Enterococcus faecalis.
Substrate selection of Christmas tree worms (Spirobranchus spp.) in the Gulf of Eilat, Red Sea

Christmas tree worms (Spirobranchus spp.) are prominent sessile organisms inhabiting hermatypic corals in tropical and sub-tropical reefs. Until recently, most of the larger Spirobranchus species were considered to be in obligatory associations with live hermatypic corals. However, recent studies indicate that some Spirobranchus species can build tubes on artificial substrate as well and that others may show preferences for using specific species of corals and hydrozoans as substrates. In the present study, we conducted a survey of Spirobranchus spp. substrate preference in the Gulf of Eilat. We found seven morphotaxa of Spirobranchus, of which two may be a single new species. We show that Spirobranchus taxa differ not only in their morphology, but also in their substrate use. Our results demonstrate that the ecological niche of Spirobranchus is species-specific, and a putative innate preference exists for some substrates.
Fungi associated with sheep hairs in Saudi Arabia

Nasser L. A. and Abdel-Sater M. A. (1997): Fungi associated with sheep hairs in Saudi Arabia. Czech Mycol. 50: 99-106 T he frequency of occurrence of fungi in 25 hair sam ples of nine kinds of sheep, collected from different localities in Saudi A rabia, was estim ated using three isolation m ethods a t 28 °C. Fortyfive species and one variety representing 23 genera were isolated and the m ost com m on genera were Chrysosporium , A ltem a ria , Aspergillus and P enicillium . T he m ost prevalent species of the above genera were C. indicum , C. tropičům , A ltem a ria a ltem ata , Aspergillus flavus, A . fum igatus. P enicillium chrysogenum and P. oxalicum. O ther fungi were also isolated with variable frequencies.
Considerazioni biogeografiche sulla coccidiofauna della Sicilia

Biogeographia vol. )OO( - 2011 (Pubblicato il 23 dicembre 2011) La Biogeograﬁa della Sicilia Considerazioni biogeograﬁche sulla coccidiofauna della Sicilia GAETANA MAZZEO, AGATINO RUSSO, POMPEO SUMA Dzpartimento di Gestione dei Sistemi Agroalimentari eAmbz'em‘alz' sez. Entomologia czgmrizz, via 5. Soﬁa 100, 95100 Catania (Italy) e-mail: gamzzzzeo @unict.z't Key words: Homoptera Coccoidea, zoogeography, distribution, corotypes. SUMMARY Results of a zoogeographical study on scale insect fauna of Sicily are provided. Homoptera Coccoidea, due to the close relationship with their hostplant, represent a case study in understanding the role of human activities in fauna changes. The 169 species recorded up to know in the Island (which represent 42% of the Italian scale insects fauna) have been divided in basic distributional patterns, in cosmopolitan or subcosmopolitan elements and in en- demic or with a restricted distributional area elements. The cosmopolitan or subcosmopolitan elements are the most numerous but have a limited zoogeographical value. They include species that moved from other countries to Sici- ly where the global warming effects on the climate allow them to establish and become pests of crops, forestry and ornamentals. Among the basic distributional patterns the species with wide distribution in the Holarctic region and those with wide a'i:trz'bution in the Mediterranean area are more numerous than the afrotropical and oriental species in the Mediterranean area and those endemic or wit}; :1 restricted’ distribzttional area. Moreover, considerations on the com- position of the fauna in relation to host plants representative of natural and anthropic environments are presented. INTRODUZIONE La Sicilia rappresenta un’area di notevole interesse zoogeografico. La sua po- sizione al centro del mar Mediterraneo e gli eventi paleogeografici e paleocli— matici che l’hanno interessata, determinandone le condizioni di insularita, fan- no si che essa rappresenti una peculiare area di studio di particolare interesse entomologico. Gli insetti ﬁtomizi quali gli Homoptera Coccoidea, in relazio- ne alle loro caratteristiche biologiche e morfologiche, rappresentano un caso particolarmente interessante. Le cocciniglie, infatti, instaurano uno stretto rap— porto con la pianta ospite sulla quale vivono per tutta la loro vita, senza possi- bilita o quasi di operare spostamenti attivi. Nella maggioranza dei Casi esse so— no dotate di arti solo negli stadi giovanili e, nei diaspini, solo nella prima eta di sviluppo; sebbene diversi studi abbiano dimostrato la possibilita di un loro spo- stamento operato dal vento (Qin et al., 1998) la dispersione per lunghe distanze
Temporal variation in survival and recovery rates of lesser scaup: A response

We recently analyzed long-term (1951–2011) continental band-recovery data from lesser scaup (Aythya affinis) and demonstrated that harvest rates declined through time, but annual survival rates exhibited no such trends; moreover, annual harvest and survival rates were uncorrelated for all age-sex classes. We therefore concluded that declining fecundity was most likely responsible for recent population declines, rather than changes in harvest or survival. Lindberg et al. (2017) critiqued our conclusions, arguing that we did little more than fail to reject a null hypothesis of compensatory mortality, postulated ecologically unrealistic changes in fecundity, and failed to give sufficient consideration to additive harvest mortality. Herein, we re-summarize our original evidence indicating that harvest has been compensatory, or at most weakly additive, and demonstrate that our analysis had sufficient power to detect strongly additive mortality if it occurred. We further demonstrate that our conclusions were not confounded by population size, band loss, or individual heterogeneity, as suggested by Lindberg et al. (2017), and we provide additional support for our conjecture that low fecundity played a major role in declining scaup populations during 1983–2006. We therefore reiterate our original management recommendations: given low harvest rates and lack of demonstrable effect on scaup survival, harvest regulations could return to more liberal frameworks, and waterfowl biologists should work together to continue banding lesser scaup and use these data to explore alternative hypotheses to identify the true ecological causes of population change, given that it is unlikely to be excessive harvest. © 2017 The Wildlife Society.