Miracle-dz/UniFAR-FTUs huggingface dataset:
Speciation and phylogeography in the New Zealand archipelago : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Evolutionary Biology at Massey University, Palmerston North, New Zealand, September 2010

New Zealand biogeography has been dominated by the knowledge that its geophysical history is continental in nature. The continental crust (Zealandia) from which New Zealand is formed broke from Gondwanaland at about 80 Ma, and there has existed a pervading view that the native biota is primarily a product of this long isolation. However, molecular studies of terrestrial animals and plants in New Zealand indicate that many taxa arrived since isolation of the land, and that diversification in most groups is relatively recent. This is consistent with evidence for species turnover from the fossil record, taxonomic affinity, tectonic evidence and observations of biological composition and interactions. Extinction, colonisation and speciation have yielded a biota in New Zealand that is in most respects more like that of an oceanic archipelago than a continent. * Published ‘Goldberg, J., Trewick, S.A. & Paterson, A.M. (2008) Evolution of New Zealand’s terrestrial fauna: a review of molecular evidence. Philosophical Transactions of the Royal Society B, 363, 3319-3334. ’ 4 II Abstract
Production and Optimization of Extracellular Amylase from Soil Receiving Kitchen Waste Isolate Bacillus sp. VS 04

3 Abstract: Amylases (EC 3.2.1.1) hydrolyses the -1,4glycosidic linkages of starch. Microbes are the most preferred sources of enzymes due to their broad biochemical diversity. The present study is focused with the isolation of amylase producers from soil receiving kitchen waste and to optimize the cultural condition for the maximum amylase production. From the 17 isolates one isolates was selected based on amylase activity and identified as Bacillus sp. The various parameters have conducted for maximum enzyme production. Production parameters were optimized as temperature (40°C), incubation period (72 h) and inoculums size (2%). Among different carbon and nitrogen source supplemented starch and yeast extract respectively showed enhanced production. In the case pH neutral pH was suitable for maximum enzyme production by Bacillus sp. The molecular weight of partially purified amylase was 84 Kda.
Antioxidant and antibacterial activity of crude methanolic extract of Euphorbia prostrata collected from District Bannu (Pakistan)

Medicinal plants help in improving the human health that is primarily due to bioactive constituents such as flavonoids, alkaloids, saponins, cardiac glycosides and tannins. These compounds play important role in minimizing oxidative stress, cancer, impotency, cardiac dysfunction and microbial inhibition. Euphorbia prostrata (L) is a small prostrate, annual herb found all over the world including Pakistan. This study was designed to investigate the protective effects of E. prostrata against oxidative stress and antibacterial potential. Methanolic extract of E. prostrata were used in three different concentrations of 1, 3 and 5 mg/ml. The maximum inhibition was shown at highest concentration of 5 and at 3 mg/ml the moderate inhibition while at 1 mg/ml the minimum inhibition was shown. Similarly concentration of methnolic extract of E. prostrata exhibited excellent scavenging activity. The % scavenging of E. prostrata is directly proportional to the concentration. The order of % scavenging activity is 50 < 100 < 150 < 200 < 250 �g/ml. Ascorbic acid is used as negative control
SPECIES‐SPECIFIC DIFFERENCES OF PYRENOIDS IN CHLORELLA (CHLOROPHYTA) 1

The structure of the pyrenoid supports the separation of Chlorella species into two groups based on cell wall chemistry and suggests evolutionary relationships. Chlorella species with a glucan‐type wall exhibit quite diverse pyrenoid structures, which may indicate that these species are not closely related. Those species with glucosamine cell walls (C. kessleri, C. sorokiniana, C. vulgaris) are virtually identical in pyrenoid morphology, indicating a closer evolutionary relationship. In the species with glucosamine walls, the thylakoid that penetrates into the pyrenoid matrix, is unijormly double‐layered. Pyrenoids in the species with glucan walls show various features: 1) a pyrenoid matrix only, 2) a pyrenoid traversed by a few discs of double thylakoids with many adhering pyrenoglobuli, 3) a pyrenoid penetrated with tubelike structures or 4) a pyrenoid penetrated with many single undulating thylakoids. The pyrenoid structure of the symbiotic Chlorella in Paramecium bursaria resembles those of free‐living Chlorella with glucosamine walls.
EUROPEAN BISON (BISON BONASUS) IN LITHUANIA: STATUS AND POSSIBILITIES OF RANGE EXTENSION

Since 1973, Lithuania has been one of few European countries with a vital free-ranging bison herd. The article analyses a current state of the bison population and problems of the last decade. Data are presented on the dynamics of numbers of fenced and free-ranging bison, bison biology features (nutrition, damage done, reproduction, changes in behaviour), territory occupied by the herd and migrations. Having analysed the reasons of failed setting free of the bison herd in Sirvintos Region, details of the project of a new bison herd in South Lithuania are provided (aims, place selection criteria, technical preconditions of successful realisation). The suitability of the Bukta forest for the range extension of the bison population is discussed along with possible problems.
Mycotic aspects of epizootic ulcerative syndrome (EUS) of Asian fishes

A survey of fish affected with epizootic ulcerative syndrome taken from outbreaks in countries throughout South and South-East Asia showed that a morphologically typical fungus was consistently present within lesions. Although the majority of the fungal mycelium was dead in most lesions it proved possible to isolate a very delicate and culturally demanding Aphanomyces from such lesions in a few cases. It also proved relatively easy to isolate other members of the Saprolegniaceae including Aphanomyces from the surface of lesions, but these were considered saprophytes derived from background spore burdens in the water. Sporangium morphology of the putatively pathogenic isolates of Aphanomyces was different from that of saprophytic Aphanomyces strains and they also had a lower thermal tolerance. When a mycelium from these strains was placed below the dermis of healthy fish, it caused an inflammatory response and proceeded to migrate down into the tissues of the fish, inducing severe myonecrosis with chronic epithelial reaction. The saprophytic isolates induced a local host response followed by healing of the induced lesion, and destruction or expulsion of the mycelium. It is considered that the specific slow-growing, thermo-labile Aphanomyces is the pathogenic fungus which causes so much tissue damage in this disease, although it may not be a primary pathogen in its own right.
How Danderous is Methyl Ethyl Ketone (MEK)? Corresponding Author:

Methyl ethyl ketone (MEK) is an organic solvent used throughout the paint and print industry. It is listed as a hazardous chemical by the United States Environmental Protect ion Agency but the neuropsychological and neuropathic effects from exposure are reported variously. Potentially, debilitating effects on occupational workers has economic as well as welfare issues; hence, there is a need to recognise and standardise assessment procedures in industry and in clinical neuropsychology.
Analysis of Genetic Diversity in Eleven Tomato (Lycopersicon esculentum Mill.) Varieties using RAPD Markers

Genetic diversity of 11 tomato ( Lycopersicon esculentum Mill.) varieties was assessed through RAPD analysis. Twenty arbitrary oligonucleotide primers used in the RAPD ‐ PCR produced a total of 584 different marker bands with an average of 29.2 bands per primer. Based on the banding pattern 94.168% polymorphism observed among the tomato varieties. Size range of amplified DNA bands varied from 0 . 1 ‐ 10 k b. A total of 15 unique bands were amplified from the genome of the 11 tomato varieties. The values of pair ‐ wise genetic distances ranged from 0.1838 - 0.9049, indicating the presence of wide genetic diversity. The dendogram constructed based on phylogenetic relationship analysis revealed that the highest genetic diversity (0.9049) found between the variety BARI Tomato 8 and RATAN whereas the lowest (0.1838) between the variety BARI Tomato 9 and MADHURI. The dendogram has segregated the 11 tomato varieties into two major clusters. RATAN and SPECIAL ‐ OP formed cluster 1 and rest 9 varieties viz . , ROMA ‐ VF, MARGLOBE, MADHURY and BARI Tomato 9, 2, 6, 14, 8 and 3 have constituted the second cluster. Plant Tissue Cult. & Biotech. 23 (1): 49 ‐ 57, 2013 (June) DOI: http://dx.doi. org/10.3329/ptcb.v23i1. 15559
Assessing the impact of within crop heterogeneity (‘patchiness’) in young Miscanthus × giganteus fields on economic feasibility and soil carbon sequestration

In Ireland, Miscanthus × giganteus has the potential to become a major feedstock for bioenergy production. However, under current climatic conditions, Ireland is situated on the margin of the geographical range where Miscanthus production is economically feasible. It is therefore important to optimize the yield and other ecosystem services such as carbon sequestration delivered by the crop. A survey of commercial Miscanthus fields showed a large number of areas with no Miscanthus crop cover. These patches can potentially lead to reduced crop yields and soil carbon sequestration and have a significant negative impact on the economic viability of the crop. The aim of this research is to assess patchiness on a field scale and to analyse the impacts on crop yield and soil carbon sequestration. Analysis of aerial photography images was carried out on six commercial Miscanthus plantations in south east Ireland. The analysis showed an average of 372.5 patches per hectare, covering an average of 13.7% of the field area. Using net present value models and a financial balance approach it was shown that patchiness has a significant impact on payback time for initial investments and might reduce gross margins by more than 50%. Total and Miscanthus‐derived soil organic carbon was measured in open patches and adjacent plots of high crop density showing significantly lower Miscanthus‐derived carbon stocks in open patches compared to high crop‐density patches (0.47Mg C ha−1 ± 0.42 SD and 0.91Mg C ha−1 ± 0.55 SD). Using geographic information system (GIS) it was shown that on a field scale Miscanthus‐derived carbon stocks were reduced by 7.38% ± 7.25 SD. However, total soil organic carbon stocks were not significantly different between open patches and high crop density plots indicating no impact on the overall carbon sequestration on a field scale over 3–4 years since establishment for these Miscanthus sites.
Antimicrobial activity of lysozyme with special relevance to milk

Lysozyme is a hydrolytic enzyme which has been purified from cells, secretions and tissues of virtually all living organisms and viruses. While this protein has been recognized to possess many physiological and functional properties, its high microbicidal activity remains, by far, the main virtue that explains the high attention of scientists and industrial stakeholders for its practical applications in medicine and food industry. Although the egg-white is the primary source for lysozyme production at industrial scale, other sources such as milk of mammals should not be overlooked, as they may contain lysozyme molecules with specific properties not present in the conventional egg-white lysozyme. This review discusses the antimicrobial activity of lysozyme with special emphasis on milk’s lysozyme, and attempts to shed some light on the recent advances elucidating the mechanism of its antimicrobial activity against sensitive microorganisms as well as the means used by some bacteria to resist such an activity.
IMPROVEMENT OF FUNCTIONAL PROPERTIES OF RAPESEED PROTEIN CONCENTRATES PRODUCED VIA ALCOHOLIC PROCESSES BY THERMAL AND MECHANICAL TREATMENTS

Plant protein products produced via alcoholic extraction procedures often show a deterioration of their functional characteristics. The aim of this study was to modify rapeseed protein concentrates (RPCs) obtained by alcoholic extraction using different treatments in order to reconstitute their functional properties and to evaluate the influences of different modification procedures. It could be shown that a heat treatment at alkaline pH resulted in significant lower emulsification capacity (232 mL/g) but led to amelioration of water binding capacity (4.9 mL/g) and emulsion stability (95%). Heat treatment was also connected with loss in protein solubility whereas homogenization at high pressure revealed maintenance of protein solubility of the RPC concurrent with a significant higher emulsion capacity (357 mL/g) and emulsion stability (83%) in comparison with the untreated RPC (335 mL/g and 56%, respectively). Homogenization technique for RPC seems to be a promising tool for the development of applications in bakery or meat products. PRACTICAL APPLICATIONS The German Federal Ministry of Education and Research project Napus 2000 investigated how the use of rapeseed could be improved. The key objectives of this project were to utilize all the rapeseed and to use modern methods of genetic engineering in combination with classical plant cultivation to improve the rape products and so make a contribution to more healthy nutrition. More than 15 famous industrial partners and scientific institutions participated in this project. The key work fields in Napus 2000 were neutral lipids, proteins, antioxidants and polar lipids. The main work area of the Fraunhofer IVV was on proteins and this work covered the development of methods to recover proteins and potential applications of the rape protein products in foods.
Evaluating Pollination Biology of Cornus florida L. and C. kousa (Buerger ex. Miq.) Hance (Cornaceae: Cornales)

Abstract Visitors to flowers of Cornus florida and C. kousa were assessed in East Tennessee during spring in 2008 and 2009. Visitation rate data were compiled throughout the flowering period of both tree species across a range of environmental conditions. Diurnal and seasonal variations in visitation are reported. Pollen coverage on collected insects was assessed to estimate pollination efficiency. In total, 11 families from 4 insect orders were collected from C. florida and 26 families from 5 insect orders were collected from C. kousa. Visitors to C. florida varied considerably across sites and between years, however bees in the families Andrenidae and Halictidae were consistently present and are expected to be key pollinators of flowering dogwood. Although halictid bees were also common visitors to C. kousa the most common visitors to Chinese dogwood were scarab, cerambycid, and cantharid beetles.
Lipoquinones in members of the family Pasteurellaceae

Selected members of the family Pasteurellaceae Pohl 1981 were investigated for their lipoquinone contents by using high-performance liquid chromatography. In addition to ubiquinones and demethylmenaquinones, menaquinones (MK-7 or MK-8 or both) were detected, mostly as minor naphthoquinone components, in several Actinobacillus, Pasteurella, and related species. Previous studies that relied on difference spectrophotometry and thin-layer chromatography did not identify menaquinone components in lipid extracts of members of the Pasteurellaceae. The view that this family can be differentiated from the Enterobacteriaceae and other fermenting gram-negative bacteria by a lack of menaquinones cannot be maintained. Although the situation seems to be more complex than previously recognized, the distribution patterns of lipoquinone structural types and their isoprenologs appear to remain a valuable chemotaxonomic tool for these bacteria.
GENIC DIFFERENTIATION AND PHYLOGENETIC RELATIONSHIPS AMONG TROPICAL HARVEST MICE (REITHRODONTOMYS: SUBGENUS APORODON)

Abstract To assess genic differentiation and phylogenetic relationships among selected species in the subgenus Aporodon, we screened 31 presumptive genetic loci in 6 species in the subgenus Aporodon (R. creper, R. gracilis, R. mexicanus, R. microdon, R. spectabilis, and R. tenuirostris) and in 4 species in the subgenus Reithrodontomys (R. chrysopsis, R. fulvescens, R. megalotis, and R. sumichrasti). The resulting phylogenetic trees were compared with the results of previous molecular and morphological studies. Results demonstrate that the subgenus Aporodon is monophyletic. Relationships determined on the basis of allozymes are largely congruent with an earlier analysis based on morphological and molecular characters. However, samples of R. mexicanus do not form a monophyletic lineage. Accordingly, populations from north-central Oaxaca and Costa Rica each likely represent an undescribed species.
The Susceptibility of Monocotyledons to Agrobacterium tumefaciens

The susceptibility of 257 monocotyledon species belonging to 139 genera and 27 families, has been tested and the literature on this subject reviewed. In contrast with dicotyledons and gymnosperms, monocotyledons are much less susceptible to Agrobacterium tumefaciens: only 3 % of the species of monocotyledons tested were host plants, whereas 60 % of the dicotyledons and gymnosperms were susceptible. Only the closely related monocotyledon orders Liliales (6 families) and Arales (1 family) contained species that were susceptible. These results are consistent with a proposed taxonomic relationship between the Liliales and the dicotyledons. A correlation between host biochemical capabilities and susceptibility to crown gall is suggested.
The endoplasmic reticulum stress response is stimulated through the continuous activation of transcription factors ATF6 and XBP1 in Ins2+/Akita pancreatic β cells

The dominant C96Y mutation of one of the two murine insulin genes, Ins2, causes diabetes mellitus in ‘Akita’ mice. Here we established pancreatic islet β cell lines from heterozygous mice (Ins2+/Akita). Western blot analysis of endoplasmic reticulum (ER) molecular chaperones indicated that Grp78, Grp94 and Orp150 are significantly increased in Ins2+/Akita cells compared with wild‐type (Ins2+/+) cells. Reporter gene assays using the human GRP78 promoter with or without the ER stress response element (ERSE) showed that Ins2+/Akita cells exhibit significantly stronger ERSE‐dependent transcriptional activity than Ins2+/+ cells. Transient over‐expression of the Ins2 C96Y mutant in wild‐type β cells induces a stronger ERSE‐dependent stress response than does wild‐type Ins2 over‐expression. The ERSE‐binding transcription factor ATF6 is strongly activated in Ins2+/Akita cells. The activity of a reporter containing the specific binding sequence of another ERSE‐binding transcription factor, XBP1, is also enhanced in Ins2+/Akita cells. Levels of active forms of XBP1 mRNA and protein are both markedly elevated in Ins2+/Akita cells. These results indicate that this cell line is subject to continuous ER stress and that the Ins2 C96Y mutation induces the expression of ER chaperones through the activation of ATF6 and XBP1.
Biology, Spawning, and Movements of Cycleptus meridionalis in the Lower Alabama River, Alabama

Abstract The goals of this study were to describe the biology, spawning season, and movements of Cycleptus meridionalis (Southeastern Blue Sucker) in the lower Alabama River, and evaluate possible spawning-site fidelity to Millers Ferry Lock and Dam. We also present fisheries, river discharge, and lock-use data in support of our recommendation to implement fish-passage operations at Claiborne and Millers Ferry locks and dams. We collected a total of 1094 Southeastern Blue Suckers—704 males, 355 females, and 35 sex-undetermined individuals—below Millers Ferry and Claiborne locks and dams from 1995 to 2005. Females were significantly longer and heavier per given total length than males. Spawning season lasted from March through April. Peak spawning occurred in mid-March when the water temperature was 15–20 °C. Age estimates ranged from 4 to 34 years for males and females. We recaptured 20% (206) of 1049 anchor-tagged fish multiple times (range = 1–10) at intervals between captures of 1–3618 d, and recaptures occurred 1–99 km downstream after release. We detected 75% (111) of 149 sonic-tagged fish 1–19 times at intervals between detections of 1–1288 d at distances of 4–250 km downstream after release. Spawning-site fidelity was confirmed by the recapture of 57 anchor-tagged fish and the detection of 15 sonic-tagged fish in or near Millers Ferry tailwater. Daily fish-passage operations completed at Claiborne and Millers Ferry locks and dams from January through April should increase upstream fish-migration success into the upper Alabama and Cahaba rivers without adversely affecting navigation, hydroelectric generation schedules, and industrial water needs along the river.
Diversity of Xiphinema species (nematoda: dorylaimida) associated with different crops in Romania

Nematodes of the genus Xiphinema (family Longidoridae) are economically important plant pests, some of them known as vectors of nepo-viruses [13]. Accurate identification of Xiphinema spp. is important in regard to their virus transmission capability. Nine species of the genus Xiphinema are reported so far from Romania. New information on the morphology and distribution of several Xiphinema species recovered from different crops and regions of Romania is provided. Soil samples were collected at a depth of 20-40 cm in the rhizosphere of various plants: grapevine, peach, apricot, alfalfa, strawberry. Based on the morphological and morphometrical characters the following species were identified: Xiphinema italiae Meyl, 1953, X. vuittenezi Luc, Lima, Weischer et Flegg, 1964, X. pachtaicum (Tulaganov, 1938) Kirjanova, 1951, X. simile Lamberti, Choleva et Agostinelli, 1983, X. taylori Lamberti, Ciancio, Agostinelli et Coiro, 1992 and X. parasimile Barsi et Lamberti, 2004. Xiphinema parasimile represents a new geographical record.