Miracle-dz/UniFAR-FTUs huggingface dataset:
Maize MADS-Box Genes Galore

MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants ranging from root to flower and fruit development. A large screening for MIKC-type MADS-box gene cDNAs in maize yielded sequences for 31 different genes, 29 of which are of the MIKC-type. 15 of these MIKC-type genes were novel. Together with three published genes for which a cDNA did not appear in our screen 32 different MIKC-type genes have thus been identified in maize now. All of these genes are members of subfamilies known from eudicots. However, it appears that in many subfamilies there are more gene members in maize than in eudicot model plants such as Arabidopsis. Phylogeny reconstructions involving all published MADS-box genes identified two major reasons for this. First, after the establishment of the defined gene subfamilies in a common ancestor of eudicots and monocots, a number of gene duplications occurred in the lineage that led to extant monocots after the eudicots had branched off, but before the separation of the lineages that led to extant maize and rice. Based on our gene collection we could estimate that there must have been at least 20 different MIKC-type genes in the most recent common ancestor of maize and rice about 50-70 million years ago. In contrast, the same data set supports only the presence of at least 11 different genes in the last common ancestor of monocots and eudicots about 200 million years ago. Second, phylogenetic trees in line with chromosomal mapping data revealed that the event that gave rise to the ancient segmental allotetraploidy of the maize genome established typically two young paralogs for many orthologous rice MADS-box genes. By chromosomal mapping also candidate genes for some interesting maize developmental gene loci could be identified. The genes reported here are a rich ressource for further studies on the evolutionary dynamics of a complex gene family, the developmental genetics of maize, and a rational crop design employing developmental control genes as tools.
Preliminary survey and diet analysis of juvenile fishes of an estuarine creek on Andros Island, Bahamas

Estuarine habitats are important nursery and feeding areas for a variety of fish and invertebrate species. Although numerous studies have investigated trophic linkages in temperate estuarine systems, few have empirically examined these relationships in tropical and subtropical estuaries (Colton and Alevizon, 1983; Heck and Weinstein, 1989; Warburton and Blaber, 1992; Ley et al., 1994; Crabtree et al., 1998). Without knowledge of dietary relationships among organisms, community structure and population interactions are difficult to deduce. To this end, a food web approach can be valuable in the study of natural communities (Polis and Winemiller, 1996). Since many tropical and subtropical estuaries are numerically dominated by juvenile fishes (Arrivillaga and Baltz, 1999), the trophic role of these life stages is especially important. Juvenile fish utilization of mangrove and seagrass habitats has been documented in the Caribbean (Robblee and Zieman, 1984; Stoner, 1986; Rooker and Dennis, 1991; Sedberry and Carter, 1993) and Florida (Thayer et al., 1987; Sheridan, 1997; Ley et al., 1999), although few studies have analyzed feeding habitats of the juvenile fishes in these areas (Heck and Weinstein, 1989; Hettler, 1989; Ley et al., 1994). To our knowledge, there have been no published studies of the distribution and diet of fishes in estuarine creeks, and associated seagrass or mangrove areas, in the Bahamian Islands. The purpose of our study was twofold: (1) identify fish species utilizing five major habitat types (sandflat, mangrove, seagrass, rocky structure and artificial structure) of an estuarine creek on Andros Island, Bahamas, and (2) provide a preliminary diet analysis of common juvenile fishes.
Growth and survival of the Indian Pearl oyster (Pinctada fucata) in Kakinada Bay

Kakinada Bay which has a total spread of 146 sq.km. area has diverse moUuscan resources, especially bivalves and gastropods. Several workers have studied in detail, the molluscan resources of the Bay and their fishery characteristics. The Bay also harbuors a population of resident pearl oyster, Pinctada chemnitzii towards its eastern side near Hope Island. But Pinctada fucata is an exogenous species as far as Kakinada Bay is concerned.
Harvest frequency and burning effects on monocultures of 3 warm-season grasses

Harvest frequency and burning can affect forage yield of monocultures of switchgrass (Panicum virgatum L.), big bluestem (Andropogon gerardii Vitman), and indiangrass [Sorghastrum nutans (L.) Nash]. Current information is based largely on results from mixed stands. A field experiment was established in 1986, and from 1988 to 1991 treatments were applied with burning in March, April, or May plus an unburned control. Growing-season yield was measured by harvesting 1 (June), 2 (June and July), or 3 (June, July, and August) times with unharvested control plots included. End-of-season standing crop from all plots was determined after plants became dormant. Treatments were applied to the same plots annually and were arranged in a split-split plot, randomized complete block design. The main plot was species, subplot was burn date, and sub-subplot was harvest frequency. Burning reduced yields (p<0.01), and yields were lowest in plots burned in May. Burning reduced yields of indiangrass most (57%) and big bluestem least (15%). In 1989, plots harvested three times produced yields similar to plots harvested once for all species. By 1991, yields of plots harvested 3 times per growing-season were reduced (P=0.08) below those of plots harvested once. Yield response of species also varied across the study. Growing-season yields in 1991 were 113, 67, and 89% of 1989 yields for switchgrass, big bluestem, and indiangrass, respectively. Regardless of burning and harvest frequency combination, switchgrass produced as much or more herbage than the other species.
Mechanisms of Multivesicular Body Biogenesis and Exosome Release

Exosomes are small vesicles with a diameter of approximately 50-100 nm that are secreted by a number of different cells and function in a multitude of intercellular signaling processes. Exosomes are thought to derive from release of intraluminal vesicles (ILVs) in multivesicular bodies (MVBs) after the fusion of MVBs with the plasma membrane.To understand the little explored molecular details of how cargoes are sorted to these subsets of ILVs in MVBs and secreted with exosomes, the transport of proteolipid protein (PLP) in Oli-neu cells, an oligodendroglial precursor cell line, was studied. We found that PLP was transported to distinct subdomains of the endosomal membrane and that the transfer of PLP into the lumen of endosomes did not depend on the function of the endosomal sorting complex required for transport (ESCRT) machinery but required ceramide formation. The purified exosomes were enriched with ceramide and inhibition of neutral sphingomyelinase activity reduced the release of exosomes. Sphingomyelin hydrolysis on the outer leaflet of phase separated giant unilamellar vesicles resulted in intraluminal budding from the lipid ordered phase. These results identified a novel lipid-dependent pathway for cargo transport to the ILVs in MVBs for exosomes formation.Rab family guanosine triphosphatases (GTPases) are regulators involved in intracellular membrane traffcking. A screen for the effects of Rab GTPase activating proteins (GAPs) on exosome release was performed. Expression of TBC1D10B, RN-tre, TBC1D10A, TBC1D10C and TBC1D15 reduced exosome secretion in a catalytic activity dependent manner. Rab35 was identified to be the target of TBC1D10A-C. Inhibition of Rab35 function impaired exosome secretion, induced accumulation of PLP containing endosomes and increased the mobility of endosomes closed to the plasma membrane, suggesting a function in MVB tethering. Furthermore, Rab35 was biochemically purified together with non-compact myelin, where MVBs were observed, providing a basis for understanding the biogenesis and functions of exosomes in the central nervous system.
&THALASSEUIA ASSOCIATED WITH a -THAlASSEMIA IN THAILAND

In Thailand a-thalassemia (thal), B-thal, hemoglobin (Hb) E and Hb Constant Spring (Hb CS) are prevalent. The incidences are 20-30% for a-thal (3.5% for a-thal-1 and 16% for a-thal-2), 3-9% for B-thal, up to 54% for Hb E and nearly 8% for Hb CS (1). Different combinations of these genes result in a spectrum of thalassemia syndromes ranging in severity from asymptomatic to intrauterine death. From the known gene frequencies the numbers of thalassemic patients per generation (total population of 50 million) are as follows: Hb Bart's hydrops fetalis 20,000; homozygous B-thal 31,250; B-tha1lHb E disease 162,500; Hb H disease (two genotypes) 200,000, making a total of 413,750. In addition, individuals may carry more than two of the abnormal genes leading to complex thalassemia syndromes such as aB-thal, AE-Bart's and EF-Bart's diseases.
Ultra-high temperature (UHT) treatment of milk: Comparison of Direct and Indirect modes of heating

UHT processing of milk and its subsequent storage causes several changes which affect the shelf-life of UHT milk although it remains 'commercially sterile'. These changes include whey protein denaturation, protein-protein interaction, lactose-protein interaction, isomerisation of lactose, Maillard browning, sulphydryl compound formation, formation of a range of carbonyl and other flavoursome compounds, and formation of insoluble substances. They ultimately reduce the quality and limit the shelf life of UHT milk through development of off-flavours, fat separation, age gelation and sedimentation. The extent of these changes depends on many factors, a major one being the type of UHT heating. This review compares the effect heating milk by direct and indirect modes on various aspects of processing and quality of UHT milk.
Differential expression and regulation of the human CD8a and CD8 chains

The CD8 glycoprotein is expressed by thymocytes, mature T cells and natural killer (NK) cells and has been implicated in the recognition of monomorphic determinants on major histocompatibility complex (MHC) Class I antigens, and in signal transduction during the course of T-cell activation. Both human and rodent CD8 antigens are comprised of two distinct polypeptide chains, alpha and beta. The majority of monoclonal antibodies (mAb) reactive with the human CD8 antigen bind the CD8 alpha chain, while a single mAb, T8/2T8-5H7, has been identified which binds to the CD8 alpha/beta heterodimer. While the two chains of CD8 have been presumed to be coordinately expressed in normal T cells, this is not always the case. Northern blot analysis of a panel of T-cell leukemias and normal cells demonstrate that CD8 alpha and CD8 beta are not invariably co-transcribed and phenotypic analysis of fresh and interleukin 2 (IL-2) expanded peripheral blood mononuclear cells (PBMC) confirm that the CD8 alpha and CD8 beta chains are differentially expressed at the cell surface. Four distinct subpopulations of CD8+ cells have been identified based on the expression of CD8 alpha/alpha or CD8 alpha/beta complexes: (1) T-cell receptor (TcR) alpha beta+ T cells which are CD8 alpha+/beta+; (2) TcR alpha beta+ T cells which are CD8 alpha+/beta-; (3) TcR gamma delta+ T cells which are CD8 alpha+/beta- and (4) natural killer (NK) cells which are CD8 alpha+/beta-. We also demonstrate the down-regulation of the CD8 alpha/beta heterodimers from the surface of a CD8+ T-cell clone following treatment with phorbol myristate acetate (PMA) while CD8 alpha/alpha homodimers remain on the cell surface. This observation demonstrates that a) a CD8+ T-cell clone can express both CD8 alpha/alpha homodimers and CD8 alpha/beta heterodimers and b) these two complexes do not have identical biological properties. Together, these data suggest that CD8 alpha/alpha and CD8 alpha/beta dimers may not subserve identical functions. The differential contribution of these two CD8 complexes should be considered in models of T-cell-mediated cytotoxicity and T-cell activation.
Growth and shank length of autosomal dwarf chicken.

A partial diallel crossing of Rhode Island Red (RIR), White Leghorn (WLH), Fayoumi (FO), Deshi (indigenous) Normal (DN) and Deshi dwarf (DD) chicken was made to produce RIR, WLH, FO, DN, DD, RIR × DD, WLH × DD and FO × DD offspring. A total 709 chicks; 75 RIR, 130 WLH, 100 FO, 70 DN, 66 DD, 80 RIR × DD, 80 WLH × DD and 108 FO × DD were reared according to genotype to study growth performance up to 18 weeks of age. At 19 weeks of age, the crossbreds; RIR × DD, WLH × DD and FO × DD were separated into normal and dwarf genetic groups on the basis of shank length and thus 11 genetic groups; RIR, WLH, FO, DN, DD, RIR × DD normal, RIR × DD dwarf, WLH × DD normal, WLH × DD dwarf, FO × DD normal and FO × DD dwarf were obtained. Day old weight was differed significantly (p 0.05). Apparently, RIR × DD and WLH × DD chicks had lowest mortality. The shank length significantly differed among genotypes at all ages regardless of sex (p<0.01) and differences among genotypes increased at older ages. Shank length of pure breeds and normal crossbreds were almost similar and much longer than that of dwarf crossbreds (p<0.01).
The hepatic acute-phase proteins α1-antitrypsin and α2-macroglobulin inhibit binding of transferrin to its receptor

Transferrin binding to human placental sites was inhibited by the acute-phase proteins alpha 1-antitrypsin (alpha 1-AT) and alpha 2-macroglobulin (alpha 2-MG), whereas haptoglobin, C-reactive protein and ferritin displayed no such effect. In equilibrium saturation binding assays, the effective acute-phase proteins decreased the apparent affinity of the binding sites for transferrin, but the transferrin binding-site density Bmax. was not significantly changed. For instance, the addition of 30 microM alpha 1-AT increased the KD of transferrin from 8.46 +/- 1.51 nM to 21.6 +/- 3.04 nM; the Bmax. values were 1.17 +/- 0.18 pmol/mg of protein and 1.04 +/- 0.25 pmol/mg of protein respectively. In kinetic studies, alpha 1-AT decreased the association rate constant k+1 of the 125I-transferrin-binding-site complex from 2.18(+/- 0.21) x 10(7) M-1.min-1 to 3.99(+/- 0.18) x 10(6) M-1.min-1. In contrast, the dissociation rate constant k-1 was not changed (0.0948 +/- 0.002 min-1, 0.089 +/- 0.0017 min-1). On isoelectric focusing, no alteration in transferrin protein pattern or shift in isoelectric point was detected in the presence of alpha 1-AT. Inhibition of transferrin binding by the acute-phase proteins alpha 1-AT and alpha 2-MG is competitive. Interestingly, inhibition is already present at physiological concentrations. However, full inhibition is only achieved at concentrations above the normal range, which are attained in acute-phase reactions.
Gender differences in risk factors, clinical presentation, and outcome of stroke: A secondary analysis of previous hospital-based study in Qatar

Objectives: The aim of this study was to describe gender differences in stroke risk factors, clinical presentation, and outcome in Qatar. Subjects and Methods: This is a secondary post hoc analysis of our previous prospective observational hospital-based study with new objective. Results: Among the 270 patients involved in this study, there were 198 (73%) males and 72 (27%) females. Two hundred and seventeen (80.4%) patients had ischemic strokes, whereas 53 (19.6%) patients had hemorrhagic stroke. Patients with hemorrhagic stroke showed no significant gender difference in their stroke profile. On the other hand, male patients with ischemic stroke were more likely to have had a history of hypertension (P < 0.001), smoking (P < 0.001), and daily alcohol drinking (P < 0.001), while female patients were more likely to have had a history of diabetes mellitus (P < 0.001). Moreover, dysarthria, swallowing problems, and gait imbalance were observed with high frequency in male patients, while headache was significantly associated with females (P < 0.001). Posterior circulation stroke syndrome was observed more in male patients, whereas female patients tend to have had partial anterior circulation syndrome. In-hospital mortality rate showed no sex differences in both hemorrhagic and ischemic strokes. Conclusions: No gender differences were found in patients with hemorrhagic stroke, whereas in patients with ischemic stroke there were significant gender differences in risk factors and clinical presentation except for fatality rate.
The contribution of wild mammals to the epidemiology of tuberculosis (Mycobacterium bovis) in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Massey University

The objective of these studies was twofold. The primary aim was to gain a better understanding of the role of free-living mammalian species, other than possums, in the epidemiology of wildlife tuberculosis in New Zealand. The other objective was to continue the operation of the Castlepoint longitudinal study so that hypotheses regarding the epidemiology of M. bovis infection in possums could be further refined and clarified. Of the wild carnivores found in New Zealand, the disease persists at high prevalence only in ferrets, and is probably maintained principally by ingestion of tuberculous carrion. Although a moderate number of ferrets excrete M. bovis orally, there appears to be only minor intraspecific transmission by bite wounding. Although cats and stoats can also become infected through scavenging, they appear to be less susceptible to oral infection than ferrets. There is no substantial evidence to suggest that any of New Zealand’s free-living carnivores are likely to be reservoir hosts of M. bovis. Observational studies involving twelve domestic red deer suggested that cervids probably become infected through close inspection and investigation of moribund tuberculous possums, and that the likelihood of exposure to M. bovis was related to the curiosity and social ranking of the deer. Necropsies conducted principally on wild red deer and involving 152 animals provided evidence to suggest that significant bacillary excretion from infected deer was uncommon, and that only the few with advanced disease had the potential to be highly infectious. However, behavioural phenomena and disease characteristics preclude the ready transmission of disease amongst cohorts. There is now strong evidence to suggest that a high prevalence of tuberculosis infection in wild deer can only be maintained through contact with infected possums. However, deer may still be able to maintain the disease amongst themselves, albeit at a low prevalence, in the absence of infection in possums. This study also confirmed the importance of lymphoepithelial tissues, such as the oropharyngeal and nasopharyngeal tonsils, as primary sites for the establishment of M. bovis infection, and the subsequent excretion of organisms in
Influence of time of application of Pseudomonas fluorescens in suppressing sheath blight of rice

The present investigation was undertaken to test the effectivity of potential strains of Pseudomonas fluorescens against sheath blight of rice under field conditions, applied as three time sequences. Foliar sprays with Pfr 1, 7 days before pathogen inoculation resulted in maximum reduction in sheath blight severity (59.6-64.4) and incidence (36.7-40.4), and increasing in grain yield (30.6-32.3) and 1000-grain weight (27.2-29.5). Simultaneous application of the bioagent(s) and R. solani or bioagents applied 7 days after inoculation with R. solani was relatively inferior in reducing the disease.
Membrane Organization and Dynamics in Mammalian Sperm

59 Introduction . 61 Experimental Methods . 63 Results . 70 Discussion . 88 Acknowledgements . 92 References . 93 Chapter Three: Membrane changes associated with capacitation . 98 Abstract . 99 Introduction . 101 Experimental Methods . 105 Results . 109 Discussion . 118 Acknowledgements. 122 References . 123 Chapter Four: Membrane properties and dynamics in sperm . 129 Abstract . 130
Phylogenetic affinities of the New Zealand blue duck (Hymenolaimus malacorhynchos)

We investigate the phylogenetic affinites of the New Zealand blue duck (Hymenolaimus malacorhynchos), a riverine specialist of uncertain relationships, using 2613 bp of DNA sequence data from 3 mitochondrial genes. Hymenolaimus has variously been considered an aberrant Anas species, or an ancient taxa in the tribe Anatini. Presently, it is placed in a highly-derived clade (Tribe Merganettini) with the shelducks. Our findings show that Hymenolaimus forms a monophyletic clade, and does not fit within any of the other duck tribes around the world. Our study also confirms convergent evolution among duck species that inhabit fast flowing rivers. Robertson, B.C.; Goldstien, S.J. 2012. Phylogenetic affinities of the New Zealand blue duck (Hymenolaimus malacorhynchos). Notornis 59 (1&2): 49-59.
A modelling approach for conservation of European Eel (Anguilla anguilla) and related fisheries

Although the main features of the continental phase of European eel’s (Anguilla anguilla) biological cycle are currently well-known, realistic and well tuned demographic models based on long-term studies are still needed. Age-length data from a 11-year monitoring of the European eel population of the Camargue lagoons (Rhone delta, Southern France) were collected for glass, yellow and silver eels. Three distinct models were calibrated to describe the growth process of undifferentiated eels, females and males, respectively. Uncertainty of parameter estimates was evaluated by bootstrapping. Females were characterized by larger asymptotic body size than males (580±50 vs. 388±13 mm) and faster growth, whilst the Brody growth coefficient was larger for males than for females (3.00·10±1.68·10 vs. 1.73·10±0.50·10). Sexual differentiation was estimated to begin at 204±38 mm, i.e., at the end of the second year of permanence in the lagoons, well before the length at which macroscopic differentiation becomes possible (about 300 mm), but consistently with histological observations. Males are likely to leave the lagoon or die (due to either natural or fishing mortality) within the first three years, whilst females can remain up to five years. Sexual differentiation and maturation have a major role in shaping the length structure of the population. Length-weight data were fitted by allometric curves (W = a L). The calibration of distinct curves for data from different years evidenced that the allometric coefficient a is subject to wider inter-annual fluctuations than the allometric exponent b. A negative correlation links average body length and allometric exponent (r = –0.58, P<<0.01).