Miracle-dz/UniFAR-FTUs huggingface dataset:
The ecology of sediment bacteria in lakes and comparisons with other aquatic ecosystems

We have analyzed our own data set as well as a number of previously published ones to examine factors related to the numbers and biomass of sediment bacteria in a variety of ecosystems. We have chosen to express sediment variables either on an areal or per unit sediment volume basis to avoid bias due to the more common standard- ization to sediment dry mass (also known as gram dry weight). Cross-system comparisons show that the amount of organic matter present and the sediment water content are im- portant to sediment bacterial abundance. The C:N ratio of the sediment organic matter, possibly reflecting organic matter quality, was found to explain variation in bacterial num- bers in addition to that explained by organic content. Over a broad range, sediment water content is related to sediment bacterial numbers in a unimodal fashion indicating dilution of sediments by water at high (> 80%) water content sites and dilution by inorganic particles at low (< 50%) water content sites. In lakes, the most important factors explaining sediment bacterial biomass were sediment water content and hydraulic flushing rate, a finding sup- ported by analysis of an independent data set of English lakes. Planktonic chlorophyll a and planktonic bacterial numbers (both reflecting autochthonous organic matter levels) were not significantly related to sediment bacterial biomass. We found that sediments overlain by epilimnetic water had significantly higher bacterial biomass than those overlain by hypolimnetic water. A strong positive relationship between macrobenthos and sediment bacterial biomass was found for lakes in Ontario and Quebec. Calculations of annual bacterial production and P:B ratios necessary to sustain the macrobenthic population, based on the observed bacterial and macrobenthic biomass and temperature at our sites, indicate that the bacterial biomass present is more than sufficient to maintain the macrobenthos. In addition, based on the observed ratios of bacterial to detrital carbon at our sites and on a range of published assimilation efficiencies for macrobenthos grazing on these carbon sources, we calculated that the mean percentage of carbon of bacterial origin assimilatable by macrobenthos at our sites is 53% with a maximum of 79% and a minimum of 12%. Our results suggest a tighter trophic linkage between sediment bacteria and macrobenthos in our lakes than in most marine habitats, as indicated by published studies. From these analyses, the general picture emerges of a decoupling between pelagic and benthic bacterial processes in lakes, the pelagic ones being driven mainly by autochthonous production and the benthic ones by allochthonous inputs.
Removal of Salt-killed Vegetation during Tidal Restoration of a New England Salt Marsh: Effects on Wrack Movement and the Establishment of Native Halophytes

A New England salt marsh undergoing tidal restoration was manipulated to improve halophyte seed dispersal and encourage the expansion of salt marsh plant communities. I created ten openings (150 m2) in an area of dead freshwater shrubs and common reed (Phragmites australis), which had been killed by saltwater inundation during tidal restoration. The dead plants presented a physical barrier to the upstream movement of waterborne seeds from halophyte species. Five of the openings were extended to the edge of the adjacent recovering salt marsh, providing a clear passageway into the plots cleared of barrier vegetation. Another five remained as isolated clearings and five uncut plots served as controls. The establishment of salt marsh plants was greatly enhanced by removing the barrier vegetation. While plots directly connected to the salt marsh yielded the highest numbers of new halophytes, isolated clearings also had a beneficial effect. These responses suggest that barrier vegetation removal can facilitate seed dispersal, colonization, and succession in a salt marsh habitat, and provides an effective alternative to standard restorative approaches such as artificial seeding and planting.
Circuit mechanisms underlying chronic epilepsy in a mouse model of focal cortical malformation

Highlights Ectopic interlaminar excitatory inputs from infragranular layers to layer 2/3 pyramidal neurons is a key component of the hyperexcitable circuitry Disrupted E/I balance was located far away from cortical malformations Dendritic inhibition from somatostatin interneurons play a key role in epileptogenesis Closed-loop optogenetic stimulation to activate remainder somatostatin interneurons irreversibly stops the spontaneous spike-wave discharges in vivo. In Brief Yang et al. report abnormal synaptic reorganization in an epileptogenesis zone in a mouse model of cortical malformation. The authors further demonstrate that spontaneous spike-wave discharges can be curbed by selectively activating somatostatin interneurons using close-loop fiber optogenetic stimulation to a small cortical region away from the microgyrus. Summary How aberrant neural circuits contribute to chronic epilepsy remains unclear. Using a mouse model of focal cortical malformation with spontaneous seizures, we dissected the circuit mechanisms underlying epileptogenesis. Spontaneous and optogenetically induced hyperexcitable bursts in vivo were present in a cortical region distal to (> 1mm) freeze-lesion induced microgyrus, instead of a region near it. ChR2-assisted circuit mapping revealed ectopic interlaminar excitatory inputs from infragranular layers to layer 2/3 pyramidal neurons as a key component of the hyperexcitable circuitry. This disrupted balance between excitation and inhibition was prominent in the cortical region distal to the microgyrus. Consistently, the synapses of both parvalbumin-positive interneurons (PV) and somatostatin-positive interneurons (SOM) to pyramidal neurons were maladaptive in a layer- and site-specific fashion. Finally, closed-loop optogenetic stimulation of SOM, but not PV, terminated spontaneous spike-wave discharges. Together, these results demonstrate highly site- and cell-type specific synaptic reorganization underlying chronic cortical epilepsy and provide insights into potential treatment strategies for this devastating neurological disorder.
Effect of Ethrel on Stem Anatomy of Ulmus Americana Seedlings

Ethrel (2-chloroethylphosphonic acid) applied in lanolin paste at concentrations of 0.4, 1.6, 6.2, or 10.8% to stems of 3-month-old Ulmus americana seedlings greatly altered stem anatomy within 41 days. Application of ethrel at 1.6% or higher concentration was followed by greatly increased bark thickness primarily as a result of an increase in the amount of phloem and intercellular spaces. Xylem increment was increased following treatment with 0.4 or 1.6% ethrel and reduced by 6.2 or 10.8% ethrel. All concentrations of ethrel increased the number of vessels, reduced vessel diameters, and induced an increase in ray width and size of the individual ray cells. Ethrel at 6.2 or 10.8% inhibited differentiation of fibres, many of which were poorly developed and contained protoplasm and nucleL Ethrel also stimulated accumulation of dark-staining organic deposits in the ray parenchyma cells, axial parenchyma cells, and immature fibres. The data indicate a role of ethylene in control of growth and anatorny of stems.
SEASONAL CHANGES IN BIOMASS YIELD, NUTRIENT INTAKE AND ITS UTILIZATION BY SHEEP MAINTAINED ON PUBLIC RANGE LAND

Seasonal changes in biomass yield of pasture and nutrient utilization pattem of sheep maintained round the year on village community grazing land (CGL) was assessed. The biomass yield of the CGL was similar in the 3 seasons (1.54q DM/ha). Animal preferred Cenchrus catherticus and Eleucine indica during rainy season whereas during winter the preference for C. catherticus increased while that of Elucine indica decreased. The CP of random pasture vegetation was 10.5% in monsoon which declined to 8.4 and 4.0% in winter and summer, respectively. with concomitant increase in cell wall constituents during the period. The CP of mouth grab samples was, however, 11.5% in monsoon and 10.0 and 7.8%, respectively, in winter and summer. The DMI of sheep decreased from monsoon (2.1 % BW) to winter (1.8% BW) and summer (1 .6% BW), while corresponding DCP intake showed significant reduction in. summer ( 15 g/head/day) compared to winter (31.1 g/head/day) and monsoon (45. 1 g/head/day). Progressive increase in maturity and lignification of plant species was reflected in gradual decline of digestibility of DM, CP, NDF, ADF, hemicellulose and cellulose from monsoon to winter and summer. It is concluded that DMI and nutrient utilization progressively decreased from monsoon to winter and summer. The DCP intake was adequate in monsoon and winter while it was grossly inadequate in summer.
Microbial Biofilms: Cultivation and Study of Biofilm Communities

The need for laboratory studies of biofilm communities If microbial ecology is to move forward, it must go beyond the reduction of the complexities of bacteria into merely isolated cell lines, enzymes, and genetic sequences. A century of pure culture studies has provided extremely detailed information on the biochemistry, physiology and genetics of bacteria. What remains to be determined is how they function as successful members of interacting communities in biofilms and how microbial communities function as components of the environment. Filling this gap in knowledge involves more than the in situ enumeration of cells, molecules, and genetic sequences. It requires that microbial communities be considered as functional units of ecological activity. Individual microorganisms are often tightly coupled with other community members through a complex network of interactions. The genetic programming of each species may be considered to be a reproductive strategy formulated over 2.5 billion years of natural selection, and intricately intertwined with the survival of other organisms (Margulis 1981). Consequently, the most rigorous measure of understanding must involve not only the cultivation of isolated cell lines, but also the successful cultivation and characterization of dynamic microbial communities, complete with their predators and parasites. End of the pure culture era The primary axiom of bacteriology is that organisms must be isolated prior to their identification and study, and prior to the description of new species (Koch 1881, 1884). This axiom is so pervasive that it impacts protozoology, mycology and algology as well as bacteriology.
Chronic administration of buspirone down‐regulates 5‐HT2 receptor binding sites

Buspirone (BuSpar®), a clinically effective anxiolytic, has been found in clinical trials to produce effects which suggest antidepressant efficacy. As antidepressants down‐regulate type 2 serotonin (5‐HT2) receptors when given chronically to laboratory animals, we investigated whether buspirone would have similar effects; the possibility that chronic buspirone administration would affect β‐adrenergic, D‐2 dopaminergic, and γ‐aminobutyric acid (GABA) receptor binding was also investigated. When chronically administered in a regimen which reflected activity in an animal model of anxiety, buspirone produced significant decreases in in vitro 5‐HT2 and β‐adrenergic receptor binding but was without effect on D‐2 dopaminergic of GABAergic binding. Ligand saturation experiments revealed that the decrease in 5‐HT2 binding was due to a decrease in the maximal concentration of binding sites. These data demonstrate that chronic administration of buspirone to animals produces effects which suggest the potential for antidepressant efficacy in clinical use.
Annotated checklist and keys to the Orthotrichaceae of Malawi, together with new country records for East Africa

Abstract This paper provides an updated checklist of the Orthotrichaceae occurring in Malawi. Six species (Groutiella tomentosa (Hornsch.) Wijk & Margad. , Macromitrium soulae Renauld & Cardot, Schlotheimia badiella Besch. , Zygodon erosus Mitt. , Zygodon intermedius Bruch & Schimp. and Zygodon reinwardtii (Hornsch.) A.Braun in B.S.G. ) are reported as new to Malawi. A key to these species is provided. Illustrations are included for the two poorly known species Macromitrium soulae and Schlotheimia badiella. In addition, Schlotheimia badiella is recorded new to Tanzania, Macromitrium sulcatum (Hook.) Brid. is recorded new to Burundi and Macromitrium serpens (Bruch ex Hook. & Grev.) Brid. is removed from the Malawi checklist but reported as new to Kenya.
Regulation of Γ‐aminobutyric acid synthesis in situ by glutamate availability

The aim of this study was to evaluate the hypothesis that γ-aminobutyric acid (Gaba) synthesis in situ is regulated by Glu availability. The Gly decarboxylase (EC 2.1.2.10) inhibitor, aminoacetonitrile (AAN), was investigated as a means of preventing the recycling of photorespiratory ammonia, thereby causing the accumulation of Glu. In vitro measurements of crude tobacco (Nicotiana tabacum L. cv. Samsun NN) leaf extracts demonstrated that AAN effectively inhibited Gaba:pyruvate transaminase (EC 2.6.1.19) activity, but not Glu decarboxylase (EC 4.1.1.15), Glu:oxaloacetate transaminase (EC 2.6.1.1) or Glu:pyruvate transaminase (EC 2.6.1.1) activities. Gly decarboxylase activity was inhibited preferentially over Gaba transaminase, and secondary effects that can lead to an inhibition of photosynthesis were minimized by the use of a short-time course of only 90 min to investigate the impact of 25 mM AAN on the steady state metabolism of [U- 14 C]Glu by young transpiring shoots of tobacco seedlings. With time, AAN treatment caused the accumulation of Gly/Asn, but not Gaba. Furthermore, AAN increased the 14 C-radioactivity in Glu, Pro and Krebs cycle organic acids, and reduced the 14 C-radioactivity in Gln and Gaba. The data provide evidence for increased flux of carbon through the Gaba shunt when the availability of Glu as a substrate for Glu decarboxylase was enhanced.
Special issue on the occasion of the 80th birthday of A. J. (Sandy) Bruce - 50 years of shrimping in the Indo-West Pacific

A. J. (Sandy) Bruce was fascinated by animal life from his schooldays in southern England (and probably earlier), with interests in birds and freshwater crustaceans which, after completing his medical degree (‘Dr’ Bruce) and then compulsory National Service in Glasgow, led Sandy to join EAMFRO (East African Marine Fisheries Research Organisation) in Zanzibar in 1959. This was his first exposure to the tropics and the rich world of coral reefs and, most importantly of course, their as yet hardly studied shrimp fauna. This was the start of an enduring fascination with Pontoniinae and other shrimp taxa, which so far (production is not declining) has resulted in the description of one new family, 63+ new genera and 250+ new species, totalling approximately 7% of global shrimp diversity. Other crustacean groups also received attention, especially in the early years, with regular contributions appearing on the taxonomy of Brachyura, Stomatopoda, Isopoda, Rhizocephala, Mysidacea, and all major lobster groups. In a scientific career spanning over five decades, Sandy has produced in excess of 300 papers, routinely publishing 6-8 titles per year, and in some years as many as 12-14. Remarkably, until 1975 when Sandy took up the directorship at Heron Island Research Station, his taxonomic research was done almost entirely at home in his ‘spare time’.
Nucleotide isotachophoretic assay: Method and application for determination of ATP/ADP ratio in several rat tissues

Separation of ATP and ADP was achieved in isotachophoresis by using malonate, inorganic phosphate (Pi), creatine phosphate and lactate as spacers, which isolate these nucleotides from other UV‐absorbing products in rat tissues. By combining isotachophoresis with enzymatic end‐point analysis of several rat tissues, calibration for ATP and ADP was achieved obtaining an operative calibration curve that allows the use of isotachophoresis as the only analytical technique in further assays. ATP and ADP quantities of rat skeletal and smooth muscle, heart, liver, kidney and lung were determined by isotachophoresis. Individual variation was also calculated by analyzing 30 animals in the same control conditions, muscular tissues showing the greatest values for ATP and ADP, whereas kidney and lung show the smaller values. ATP/ADP ratio is discussed as a representative parameter for describing the energy content in biological tissues, there are also experimental reasons which imply that other product concentrations in this parameter not be included. This ATP/ADP ratio is calculated in the rat tissues studied, as well as its individual variation, obtaining the larger values for muscular tissues and the smaller for kidney. A great individual variation is found in kidney, followed by heart and skeletal muscle, and the most constant values are found in liver and smooth muscle. The results obtained in this calibration method for isotachophoresis assay suggest the use of a similar procedure in order to apply this technique for other nucleotide analysis.
Comparative reproductive biology of the six species of Rhododendron (Ericaceae) in Hong Kong, South China

Six rhododendron species grow wild in Hong Kong: Rhododendron farrerae Tate and Rhododendron simsii Planch. are common and widespread, Rhododendron moulmainense Hook. f. is restricted, and Rhododendron championiae Hook. f. , Rhododendron hongkongense Hutch. , and Rhododendron simiarum Hance are rare. The length and timing of the flowering period varied between species, but peak flowering for all was between late February and early May, when weather is variable and unpredictable. All species were more or less self-sterile, had sucrose-dominated nectar, and were visited by diverse insects, of which Apis cerana, Bombus eximius, and Xylocopa spp. are the major pollinators. Seeds of all species, except R. simiarum, had a light requirement for germination. There were large differences between species in the pollen/ovule ratio (176-1343), daily nectar production (0.9-38.7 µL per flower), large bee visits (0.35-4.28 per flower per 100 h) and total visits (0.92-14.53), mean seed production per flower (2-135) and per.
A Whole Genome Association Study to Detect Loci Associated with Somatic Cell Score in Dairy Cattle

One of the primary characteristics of a robust dairy cow is its disease resistance. Mastitis is considered one of the most prevalent and costly production diseases in the current dairy industry (Seegers et al. (2003)). Mastitis resistance has become part of the breeding objective in many countries (Rupp and Boichard (2003)), for economical reasons as well as to improve animal welfare (Schulman et al. (2009)). However, only a few countries routinely record mastitis, making direct selection for resistance against mastitis difficult. Further, the heritability for mastitis is generally low. Somatic cell count (SCC), which is usually logtransformed to somatic cell score (SCS), is often used in selection as an indirect measure of mastitis (Rupp and Boichard (2003)). SCC is recorded routinely in most milk recording systems. Moreover, the heritability of SCC is higher than that of mastitis and moderate to high positive genetic correlations between SCC and the occurrence of mastitis exist. An unfavorable genetic correlation between mastitis resistance and production traits (Rupp and Boichard (2003)), has made SCC a difficult trait to genetically improve (Baes et al. (2009)), despite the large genetic variation that exists in SCC (Rupp and Boichard (2003)). Breeding for increased mastitis resistance could benefit from using genomic information.
Polymers for Tissue and Organ Culture

lthough many types of diseases can be successfully cured by whole Aorgan transplantation, the overall success of this strategy clinically is severely limited by the availability of donor organs. For example, liver disease accounted for 30,000 deaths in the United States in 1989, but only 2160 liver transplants were performed [1]. Alternatives to liver transplants, such as extracorporeal circulation through devices containing liver cells, may provide temporary relief for acutely ill patients but are not suitable as a permanent replacement for liver function. Because the normal human liver regenerates completely within weeks in vivo even if greater than half is surgically removed, it should be possible to greatly expand the donor pool for liver transplants if a technique for transplanting a portion of a living donor’s liver were developed. The anatomy of the liver prevents this from being accomplished by purely surgical means in most cases; partial liver transplants using living donors have been performed in a handful of cases, but are high risk and limited to children under 20 kg.
DNA-based identification of South Korean Megaloptera larvae with taxonomic notes

Abstract Mitochondrial DNA (mtDNA) sequences, which serve as DNA barcodes, have been used to associate immature and adult stages of insects and to delineate species. The partial mitochondrial cytochrome c oxidase subunit I (COI) gene sequences for South Korean Megaloptera (all known in the adult stage) were tested to identify undetermined larvae as a rapid and effective method from 31 specimens (16 adults and 15 larvae). The COI gene sequences distinguished all six known Megaloptera species, with a low genetic distance between larvae and adults (0.50±0.21%). Based on the COI gene sequences, we associated five types of larvae with known adults including the following four species of newly described larval stages: Sialis annae Vshivkova, 1979 (Megaloptera: Sialidae); Neochauliodes formosanus (Okamoto, 1910) (Megaloptera: Corydalidae); Parachauliodes asahinai Liu et al., 2008 (Megaloptera: Corydalidae); and Protohermes xanthodes Navás, 1913 (Megaloptera: Corydalidae). The known larval stage of Sialis koreana Jung and Bae, 2012 (Megaloptera: Sialidae) was confirmed, and the morphological variation in the male genitalia of Sialis longidens Klingstedt, 1932 (Megaloptera: Sialidae) is discussed. A larval key to the six South Korean species of Megaloptera is provided.
Characteristics and functional properties of wheat germ protein glycated with saccharides through Maillard reaction

Summary The Maillard reaction (MR) under wet reaction conditions with several common saccharides, such as xylose, glucose, lactose, dextran and maltodextrin, were applied to improve the functional properties of wheat germ protein (WGP). The MR products (MRPs) prepared with dextran at pH 11.0 heated at 90 °C in 2% aqueous dispersions heating for 20 min showed better solubility and emulsifying properties. The fluorescence intensity analysis proved the MR occurred, and thinner sheet MRPs were observed by scanning electron microscope (SEM). The relative contents of Cys, Lys and Arg were decreased, which could reduce the chance of protein aggregation through -S-S bonds. Circular dichroism (CD) spectrum expressed the difference in the secondary structures between WGP and MRPs, which may make MRPs show better functional properties than WGP. These results suggested that MR with dextran under wet reaction conditions can be a promising way to improve functional properties of WGP.