Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi‐site generalised dissimilarity modelling: using zeta diversity to differentiate drivers of turnover in rare and widespread species

Generalised dissimilarity modelling (GDM) applies pairwise beta diversity as a measure of species turnover with the purpose of explaining changes in species composition under changing environments or along environmental gradients. Beta diversity only captures turnover across pairs of sites and, therefore, disproportionately represents turnover in rare species across communities. By contrast, zeta diversity, the average number of shared species across multiple sites, captures the full spectrum of rare, intermediate and widespread species as they contribute differently to compositional turnover. We show how integrating zeta diversity into GDMs (which we term multi‐site generalised dissimilarity modelling, MS‐GDM), provides a more information rich approach to modelling how communities respond to environmental variation and change. We demonstrate the value of including zeta diversity in biodiversity assessment and modelling using BirdLife Australia Atlas data. Zeta diversity values for different numbers of sites (the order of zeta) are regressed against environmental differences and distance using two kinds of regressions: shape constrained additive models and a combination of I‐splines and generalised linear models. Applying MS‐GDM to different orders of zeta revealed shifts in the importance of environmental variables in explaining species turnover, varying with the order of zeta and thus with the level of co‐occurrence of the species and, by extension, their commonness and rarity. In particular, precipitation gradients emerged as drivers in the turnover of rare species, whereas temperature gradients were more important drivers of turnover in widespread species. Appreciation of the factors that drive compositional turnover across multiple sites is necessary for accommodating the full spectrum of compositional turnover across rare to common species. This extends beyond understanding drivers for pairwise beta diversity only. MS‐GDM provides a valuable addition to the toolkit of GDM, with further potential for survey gap analysis and prediction of species composition in unsampled sites.
Characterization of Five Microsatellite Markers For Genetic Diversity Structure Analysis of Walnut (Juglans Regia L) in Five Village in Duhok Province

Five microsatellites markers (WGA202, WGA009, WGA332, WGA225 and WGA069) were used to characterize Persian walnuts (Juglans regia L.) populations in five villages (Sharanesh, Bedohe, Kanizarke (Akre), Kashane and Kuzo) of Duhok province. The microsatellites amplified (PCR products) a total of 186 alleles across all populations. The number of alleles per locus ranged from 4 alleles in Sharanesh and Kashane populations to 10 alleles also in Sharanesh and Kashane populations, with an average of 7.4. The molecular sizes of the amplified bands ranged from 158 bp to 289 bp in all populations. The observed heterozygosity (Ho) within populations ranged from 0.59 at WGA225 to 0.65 in the locus WGA202 with an average of 0.61. The PIC value (0.88) indicated that all markers were highly informative and useful for genetic diversity studies in these populations. The proportion of genetic variation presented among populations accounted for 8.4% of the total genetic diversity so it indicated a moderate level of genetic diversity between populations. The Fis average 0.24 indicated that, there was a regular tendency toward heterozygote deficiency and indicated the presence of inbreeding within the populations. The phylogenetic analysis or unrooted neighbor-joining tree highlighted the genetic distance among those five populations and separated them into two main groups placing each population according to its genetic background. The first group consists of populations Bedohe and Sharanesh in one subgroup and Kashane in second subgroup. The second group consists of populations Akre and Kuzo.
Insights on PUFA-containing lipid membranes probed by MD simulations

Author: Leng, Xiaoling . Ph.D. Institution: Purdue University Degree Received: May 2017 Title: Insights On PUFA-Containing Lipid Membranes Probed By MD Simulations Major Professor: Stephen Wassall The cell membrane serves as a barrier between the interior and exterior of a living cell. Its main structural component is the lipid bilayer, which is composed of various kinds of lipids that segregate into domains. These lipid domains, distinguished in composition and physical properties from the bulk lipids that surround them, are believed to modulate the function of resident proteins by providing an appropriate lipid environment. Polyunsaturated fatty acids (PUFA) are a type of fatty acid that contain multiple C=C double bonds. They have a lot of health benefits, which may originate in part due to their incorporation into lipids in the plasma membrane. Hypotheses that PUFA-containing lipids laterally separate into domains and/or modulate the structure of existing domains have been raised to explain the fundamental role played by PUFA. In our research, we use molecular dynamics (MD) simulations to simulate model membranes composed of PUFA-containing phospholipids and to investigate their interaction with cholesterol and vitamin E that are influential membrane constituents. The presumptive function for vitamin E in membranes is to protect PUFA against oxidation. Although the chemistry of the process is well established, the role played by the molecular structure that we address with atomistic molecular dynamics (MD) simulations remains controversial. We compared the behavior of vitamin E in lipid bilayers composed of 1-stearoyl-2-docosahexaenoylphosphatidylcholine (SDPC, 18:0-22-6PC) and 1stearoyl-2-oleoylphosphatidylcholine (SOPC, 18:0-18:1PC) via all-atom MD simulations at 37° C. SDPC represents a PUFA-containing lipid, and SOPC serves as monounsaturated control. From the calculation of van der Waals energy of interaction between vitamin E and fatty acid (FA) chains, we found higher probability that the PUFA chains surround the chromanol head group on vitamin E. This is further demonstrated by probability density maps of acyl chains around vitamin E molecules. Also, an ability to more easily penetrate
Antimicrobial activities and mineral profile of selected wild plant Linum usitatissimum in Khyber Pakhtunkhwa, Pakistan

The current study was conducted to investigate the possible potential of Linum usitatissimum in the removal of various human ailments and its mineral profile, as widely distributed in different areas of Khyber Pakhtunkhwa, Pakistan. The preliminary analytical investigation is to confirm the antimicrobial significance of L. usitatissimum, due to the presence of certain bioactive compounds. It was observed that L. usitatissimum exhibit broad spectrum activity against pathogenic bacterial strains were Agrobacterium tumefaciens sp. , Bacillus subtilis sp. , Clavibacterm ichiganensis sp. , Escherichia coli sp. , Staphylococcus aureus sp. and Xanthomonas campestris sp. While fungal strains including, viz: Aspergillus flavus sp. , Aspergillus niger sp. , Trichoderma harzianum sp. ,Fusarium oxysporum sp. , and Paecilomyces sp. Among all the bacterial strains highest inhibitory zone was recorded against B. subtillis (60.71%) followed by S. aureus (48.14%) and E. coli (44.0%) whereas no activity was observed against A. tumefaciens, C. michiganensis and X. compestris. Among all the fungal isolates highest inhibitory zone was observed against T. harzianum (76.0%) as compared to F. oxysporum (65.21%) and A. niger (57.89%) while A. flavus and Paecilomyces sp. , showed complete resistance. The results showed that elemental composition of L. usitatissimum contain significant amount of carbon (63.39%) followed by oxygen (33.90%), silicon (0.45%), potassium (0.44%), calcium (0.36%), sodium (0.30%), magnesium (0.25%), sulfur (0.24%), phosphorus (0.21%), chlorine (1.9%), iron (0.18%) and aluminum (0.15%). It was concluded from the results the said plant exhibits promising antimicrobial activity and possess sufficient amount of minerals therefore it should be exploited in traditional health care medicine for the treatment of various ailments.
Cross-Resistance of Eclipta (Eclipta prostrata) in China to ALS Inhibitors Due to a Pro-197-Ser Point Mutation

Eclipta, widespread in tropical, subtropical, and temperate regions, is one of the main malignant broadleaf weeds and thrives in moist and dryland fields. Field rates of acetolactate synthase (ALS) inhibitors have failed to control eclipta in some farmlands in China. One ALS inhibitor–resistant population (R) collected from Jiangsu province in China was confirmed in the greenhouse in our preliminary work. Whole-plant assays revealed that this R population was highly resistant to four sulfonylureas (pyrazosulfuron-ethyl, 134-fold; bensulfuron-methyl, 172-fold; metsulfuron-methyl, 30-fold; and tribenuron-methyl, 195-fold), two triazolopyrimidines (pyroxsulam, 98-fold; penoxsulam, 30-fold), and one pyrimidinylthio-benzoate (bispyribac-sodium, 166-fold) and was moderately resistant to two imidazolinones (imazethapyr, 10-fold; imazapic, 19-fold). ALS enzyme-activity assays showed insensitivity of the ALS from the R population (resistance index values ranged from 12 to 293) to all of the above ALS inhibitors in vitro. Chromatograms from ALS gene sequence analysis detected a homozygous Pro-197-Ser amino acid substitution in the R population. These results confirmed that the Pro-197-Ser substitution results in broad-spectrum cross-resistance to ALS inhibitors in the eclipta R population. To our knowledge, this study is the first to report broad cross-resistance to ALS inhibitors in eclipta and to obtain the full-length ALS gene sequence. Nomenclature: bensulfuron-methyl; bispyribac-sodium; imazapic; imazethapyr; metsulfuron-methyl; penoxsulam; pyrazosulfuron-ethyl; pyroxsulam; tribenuron-methyl; eclipta, Eclipta prostrata (L.) L.
Isolation of antagonistic fungi and evaluation of antifungal activity of the separated metabolite against the red rot of sugarcane pathogen

Antagonistic potential of six rhizosphere soil fungi viz., Trichoderma harzianum, T. viride, Aspergillus flavus, A. fumigatus, A. niger, and A. sulphureus were tested against the red rot of sugarcane pathogen Colletotrichum falcatum. Out of the seven soil fungi tested, Trichoderma harzianum was found to be most effective in controlling the growth of Colletotrichum falcatum based on the colony interactions and effects of volatile and non-volatile metabolites. When HPLC fractionation of the mycelia extract of T. harzianum, T. viride, Aspergillus flavus, A. fumigatus, A. niger, and A. sulphureus were tested against the red rot of sugarcane pathogen C. falcatum. The T. harzianum peak at showed RT 4.893 maximum antifungal activity with the inhibition zone of 0.9 mm followed by Trichoderma viride(0.7mm), A. fumigatus (0.5 mm), A. niger (0.5mm), A. flavus ( 0.4 mm), and A. sulphureus (0.3mm). This peak may be responsible for the antifungal activity of this fraction. The fungus isolated in the present study may be exploited commercially to biocontrol this disease. Further studies on the determination of the actual biochemical compound responsible for antagonistic effect through FT-IR and GC-MS analysis is under way.
When is translocation required for the population recovery of old‐growth epiphytes in a reforested landscape?

It is often assumed that species recolonization follows from the restoration of key habitat structure. Thus, forest restoration focuses on the recovery of trees into deforested landscapes, so that a multitude of associated organisms can achieve “colonization credit” and recolonize from remnant source populations into restored habitat. This opportunity for recolonization exists because species vulnerable to habitat loss may experience an “extinction debt,” during which their remnant populations decline only slowly to equilibrium with a deforested landscape. These persistent but declining populations become propagule sources for recolonization. To test limits to “colonization credit,” this study focused on old‐growth dependent lichen epiphytes, using a simulation to identify a hypothetical threshold at which: (1) the number of remnant populations, and (2) their population sizes, are too low to achieve recolonization and population recovery, despite efforts placed into forest restoration. The results show that for a landscape scenario relevant to the industrialized temperate zone, with less than 5% of old‐growth forest remaining, and ambitions for restoration to circa 10–15% forest cover, there is a failure to achieve population recovery over long timescales (i.e. within 600 years), making translocation a necessary option. This delay represents a “colonization deficit” that may be a common feature in ecological restoration more generally.
Teaching Biology in the Field: Importance, Challenges, and Solutions

Learning that occurs in a field setting is a powerful experience that promotes the development of new generations of creative scientists, enhances environmental literacy, and instills social responsibility in our citizens. Institutional challenges to field studies include decreasing financial resources and increasing regulatory concerns. These are coupled with changing student interests, in particular the growing misconception that field study is not relevant to many biological careers. Collectively, these factors contribute to a significant decline in field-study opportunities for students and lack of pedagogical guidance for instructors interested in conducting field courses. Nature and culture are inextricably linked, and we all benefit from including diverse backgrounds and perspectives in field experiences. We suggest expanding the definition of “the field” to include human-influenced ecosystems, as well as more conventional natural habitats. More than ever, the world needs the passion, insight, and wisdom that come from field studies.
Model-assisted phenotyping by digital images in papaya breeding program

Manual phenotyping for papaya Carica papaya (L) breeding purposes limits the evaluation of a great number of plants and hampers selection of superior genotypes. This study aimed to validate two methodologies for the phenotyping of morpho-agronomic plant traits using image analysis and fruit traits through image processing. In plants of the ‘THB’ variety and ‘UENF/Caliman-01’ hybrid two images (A and B) were analyzed to estimate commercial and irregularly shaped fruits. Image A was also used in the estimation of plant height, stem diameter and the first fruit insertion height. In ‘THB’ fruits, largest and smallest diameters, length, and volume were estimated by using a caliper and image processing (IP). Volume was obtained by water column displacement (WCD) and by the expression of ellipsoid approximation (EA). Correlations above 0.85 between manual and image measurements were obtained for all traits. The averages of the morpho-agronomic traits, estimated by using images, were similar when compared to the averages measured manually. In addition, the errors of the proposed methodologies were low compared to manual phenotyping. Bland-Altman's approach indicated agreement between the volume estimated by WCD and EA using caliper and IP. The strong association obtained between volume and fruit weight suggests the use of regression to estimate this trait. Thus, the expectation is that image-based phenotyping can be used to expand the experiments, thereby maintaining accuracy and providing greater genetic gains in the selection of superior genotypes.
Comparative Study of Expansion and Proliferation of Adult Mice Mesenchymal Stem Cells Derived from Bone Marrow and Adipose Tissue

The importance of Mesenchymal stem cells (MSCs) represents a favorable tool for new clinical concepts in supporting tissue engineering and cellular therapy. Bone marrow (BM) was considered important source contain mesenchymal stem cells . Another promising source of MSCs is adipose tissue (AT). MSCs derived from these sources compared regarding morphology, the success rate of isolating MSCs, expansion potential by rate of colony forming and immune phenotype. The obtained results from this study showed no obvious considerable differences concerning the morphology and immune phenotype of the MSCs derived from these sources were obvious. Differences observed concerning to the success rate of isolating MSCs, which was approximately more than 90% for BM, while it reached about 70% for AT after seven days of culturing, as well as the rate of colony forming was lower in AT cells in comparison to that obtained in BM at the same period. However, AT-MSCs could be required longest time to complete monolayer confluence, whereas BM-MSCs had the shortest proliferation period. Cells from both sources determined according to immunohistochemistry by CD105 + and CD34. ̄ Conclusions revealed that MSCs can easily and successfully obtained from bone marrow and adipose tissues, and both tissues appears suitable sources of stem cells for potential use in regenerative medicine, repairing damaged tissue nevertheless the BM-MSCs more effectual in expansion and proliferation.
The possibility of trophic transfer of neonicotinoid insecticides from crop plants to Pterostichus melanarius (coleoptera: Carabidae) via prey

1. Neonicotinoids are the newest class of insecticides and there is ongoing research about their effects on beneficial species, including natural enemies. Because of their prevalence and variety of application methods, there are many different potential routes of exposure to non-target insects. Ground beetle Pterostichus melanarius L. is an important polyphagous predator of agricultural ecosystems and previous research has shown that this and other species of ground beetles are susceptible to neonicotinoids. 2. I conducted a simple experiment to test if toxicity from thiamethoxam, one of the principal neonicotinoids, can be transferred from black cutworms (Agrotis ipsilon), a target pest, to P. melanarius, a non-target predator, through predation. Black cutworms suffered high mortality rates after ingesting thiamethoxamtreated corn seedlings, but no significant mortality differences were seen between experimental groups of P. melanarius that had fed on dead toxified cutworms and the control groups. However, some indications of sub-lethal effects were seen in P. melanarius that had fed on toxic prey, from which the beetles recovered after
Tropical household ants species composition and distribution in rapid urbanization area in Penang, Malaysia

Ants are social insects that are commonly found in tropical ecosystems and have adapted well to the urban environment. They are among the most prevalent pests in households. This study demonstrates the abundance and prevalence of structure infesting ants in residential buildings in Penang Island, Malaysia. Three locations situated in urban, suburban and rural areas were surveyed. In each area, 15 houses were assessed using modified baiting method by using 15ml centrifuge tube baited with peanut butter (13.9% protein and 41% fat) and honey (75% carbohydrate). Two collections were performed, one in the daytime and one at night, with five samples used in each period, totalling ten samples for one house. The top five most common household ants species found from the surveyed houses are P. longicornis (22.09%), T. indicum (17.74%), T. melanocephalum (17.0%), M. pharaonis (10.61%), and Pheidole spp. (5.22%). The data generated from the study will provide background information for the management of household ants in Malaysia and its neighbouring countries in the years to come.
Towards a dated molecular phylogeny of the Tanypodinae (Chironomidae, Diptera)

Abstract. A dated molecular phylogeny is proposed for the Tanypodinae, a diverse subfamily of Chironomidae (Diptera). We used molecular data from fragments of one ribosomal gene (28S), one nuclear protein-coding gene (CAD), and one mitochondrial protein-coding gene (COI), analysed using mixed model Bayesian and maximum likelihood inference methods. All proposed tribes were sampled, namely, Anatopyniini, Clinotanypodini, Coelopyniini, Fittkauimyiini, Macropelopiini, Natarsiini, Pentaneurini, Procladiini and Tanypodini. A multilocus dataset of 1938 characters was compiled from 123 individuals including outgroups. Monophyly was supported for all tribes although some relationships were not robust. Relationships between tribes and some genus groups are highly congruent with a morphology-based estimate. Relationships within tribe Pentaneurini mostly find weak support, yet previously hypothesised groupings and monophyly or lack thereof in well-sampled genera are revealed. The tempo of diversification of the family was deduced by divergence time analysis (BEAST). Origination of a subfamily stem group in the late Jurassic to early Cretaceous was inferred, with all tribes and many genera of Pentaneurini originating and diversifying in the Cretaceous. Some nodes are biogeographically informative. Gene sections supported the backbone, but more extensive sampling is needed to estimate shallower phylogenies and to better understand the tempo and diversification of Tanypodinae.