A Study of the Microbial Community at the Interface between Granite Bedrock and Soil Using a Culture-Independent and Culture-Dependent Approach

The dissolution of minerals plays an important role in the formation of soils and sediments. In nutrient limiting soils, minerals constitute a major reservoir of bio-essential cations. Of particular interest is granite as it is the major rock type of the continental land mass. Although certain bacteria have been shown to enhance weathering of granite-forming minerals, little is known about the dissolution of granite, at the whole rock scale, and the microbial community involved. In this study, both culture-independent and culture-dependent approaches were used to study the bacterial community at the interface between granite bedrock and nutrient limiting soil in Dartmoor National Park, United Kingdom. High throughput sequencing demonstrated that over 70% of the bacterial population consisted of the bacterial classes Bacilli, Beta-proteobacteria and Gamma-proteobacteria. Bacteria belonging to the genera Serratia, Pseudomonas, Bacillus, Paenibacillus, Chromobacterium and Burkholderia were isolated from the sample site. All of the isolates were able to grow in a minimal growth medium, which contained glucose and ammonium chloride, with granite as the sole source of bio-essential elements. Sixty six percent of the isolates significantly enhanced basalt dissolution (p < 0.05). Dissolution of Si, K, Ca and Mg correlated with production of oxalic acid and acidification. The results of this study suggest that microorganisms in nutrient limiting soils can enhance the rate of granite dissolution, which is an important part of the biogeochemical cycle

Chromium (VI) Inhibition of Low pH Bioleaching of Limonitic Nickel-Cobalt Ore

Limonitic layers of the regolith, which are often stockpiled as waste materials at laterite mines, commonly contain significant concentrations of valuable base metals, such as nickel, cobalt, and manganese. There is currently considerable demand for these transition metals, and this is projected to continue to increase (alongside their commodity values) during the next few decades, due in the most part to their use in battery and renewable technologies. Limonite bioprocessing is an emerging technology that often uses acidophilic prokaryotes to catalyse the oxidation of zero-valent sulphur coupled to the reduction of Fe (III) and Mn (IV) minerals, resulting in the release of target metals. Chromium-bearing minerals, such as chromite, where the metal is present as Cr (III), are widespread in laterite deposits. However, there are also reports that the more oxidised and more biotoxic form of this metal [Cr (VI)] may be present in some limonites, formed by the oxidation of Cr (III) by manganese (IV) oxides. Bioleaching experiments carried out in laboratory-scale reactors using limonites from a laterite mine in New Caledonia found that solid densities of ∼10% w/v resulted in complete inhibition of iron reduction by acidophiles, which is a critical reaction in the reductive dissolution process. Further investigations found this to be due to the release of Cr (VI) in the acidic liquors. X-ray absorption near edge structure (XANES) spectroscopy analysis of the limonites used found that between 3.1 and 8.0% of the total chromium in the three limonite samples used in experiments was present in the raw materials as Cr (VI). Microbial inhibition due to Cr (VI) could be eliminated either by adding limonite incrementally or by the addition of ferrous iron, which reduces Cr (VI) to less toxic Cr (III), resulting in rates of extraction of cobalt (the main target metal in the experiments) of >90%

A culture-independent and culture-dependent study of the bacteria community from the bedrock soil interface

In nutrient limited soils, minerals constitute a major reservoir of bio-essential elements. Consequently, the release of nutritive elements during weathering is crucial. Bacteria have been shown to enhance weathering rates; however, there has been limited work that has focused on the bacterial weathering of bedrock or parent rock, which are the major sources of minerals, in nutrient limiting soils. In this study, both a culture-independent and culture-dependent approach was used to study the bacterial community at the interface between basaltic bedrock and nutrient limiting soil in Cadiar Idris region of Snowdonia National Park, United Kingdom. High throughput sequencing method, Ion Torrent, was used to characterise the bacterial community, which generated over 250,000 sequences. Taxonomical assignment demonstrated that approximately 50% (125,000 sequences) of the community consisted of the orders Actinomycetales, Burkholderiales, Clostridales, Bacillales, Rhizobiales and Acidobacterium, with unclassified sequences representing 44% ± 1.46% (110,000 ± 3650). Bacteria belonging to the genera Serratia, Pseudomonas, Bacillus, Paenibacillus, Chromobacterium, Janthinobacterium, Burkholderia and Arthrobacter, were isolated from the sample site. All of the isolates were able to grow in a minimal growth medium, which contained glucose, ammonium chloride with basalt as the sole source of bio-essential elements. Seventy percent of the isolates significantly enhanced basalt dissolution (p < 0.05). The rate of dissolution correlated to the production of oxalic acid and acidification of the growth medium. The findings of this work suggest that at the interface between bedrock and soil heterotrophic members of the bacterial community can enhance weathering, an essential part of biogeochemical cycling in nutrient limiting soil

A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals.

The need for international collaboration in rodent pathology has evolved since the 1970s and was initially driven by the new field of toxicologic pathology. First initiated by the World Health Organization's International Agency for Research on Cancer for rodents, it has evolved to include pathology of the major species (rats, mice, guinea pigs, nonhuman primates, pigs, dogs, fish, rabbits) used in medical research, safety assessment, and mouse pathology. The collaborative effort today is driven by the needs of the regulatory agencies in multiple countries, and by needs of research involving genetically engineered animals, for "basic" research and for more translational preclinical models of human disease. These efforts led to the establishment of an international rodent pathology nomenclature program. Since that time, multiple collaborations for standardization of laboratory animal pathology nomenclature and diagnostic criteria have been developed, and just a few are described herein. Recently, approaches to a nomenclature that is amenable to sophisticated computation have been made available and implemented for large-scale programs in functional genomics and aging. Most terminologies continue to evolve as the science of human and veterinary pathology continues to develop, but standardization and successful implementation remain critical for scientific communication now as ever in the history of veterinary nosology

Hypoxia-inducible factor-1 (HIF-1) pathway activation by quercetin in human lens epithelial cells

Quercetin is a dietary bioflavonoid which has been shown to inhibit lens opacification in a number of models of cataract. The objectives of this study were to determine gene expression changes in human lens epithelial cells in response to quercetin and to investigate in detail the mechanisms underlying the responses. FHL-124 cells were treated with quercetin (10 µM) and changes in gene expression were measured by microarray. It was found that 65% of the genes with increased expression were regulated by the hypoxia-inducible factor-1 (HIF-1) pathway. Quercetin (10 and 30 µM) induced a time-dependent increase in HIF-1a protein levels. Quercetin (30 µM) was also responsible for a rapid and long-lasting translocation of HIF-1a from the cytoplasm to the nucleus. Activation of HIF-1 signaling by quercetin was confirmed by qRT–PCR which showed upregulation of the HIF-1 regulated genes EPO, VEGF, PGK1 and BNIP3. Analysis of medium taken from FHL-124 cells showed a sustained dose-dependent increase in VEGF secretion following quercetin treatment. The quercetin-induced increase and nuclear translocation of HIF-1a was reversed by addition of excess iron (100 µM). These results demonstrate that quercetin activates the HIF-1 signaling pathway in human lens epithelial cells

Effect of Oestrogen During Menopause on Risk and Age at Onset of Alzheimer's Disease

Background Oestrogen use by postmenopausal women has many health benefits, but findings on the effect of oestrogen in Alzheimer's disease are conflicting. Oestrogen promotes the growth and survival of cholinergic neurons and could decrease cerebral amyloid deposition, both of which may delay the onset or prevent Alzheimer's disease. To investigate whether use of oestrogen during the postmenopausal period affects the risk of Alzheimer's disease, we studied 1124 elderly women who were initially free of Alzheimer's disease, Parkinson's disease, and stroke, and who were taking part in a longitudinal study of ageing and health in a New York City community. Methods Relative risks and age-at-onset distributions were calculated from simple and adjusted Cox proportional hazards models. Standard annual clinical assessments and criterion-based diagnoses were used in follow-up (range 1–5 years). Findings Overall, 156 (12·5%) women reported taking oestrogen after onset of menopause. The age at onset of Alzheimer's disease was significantly later in women who had taken oestrogen than in those who did not and the relative risk of the disease was significantly reduced (9/156 [5·8%] oestrogen users vs 158/968 [16·3%] non-users; 0·40 [95% CI 0·22–0·85], p<0 01), even after adjustment for differences in education, ethnic origin, and apolipoprotein-E genotype. Women who had used oestrogen for longer than 1 year had a greater reduction in risk; none of 23 women who were taking oestrogen at study enrolment has developed Alzheimer's disease. Interpretation Oestrogen use in postmenopausal women may delay the onset and decrease the risk of Alzheimer's disease. Prospective studies are needed to establish the dose and duration of oestrogen required to provide this benefit and to assess its safety in elderly postmenopausal women

A primordial 15N-depleted organic component detected within the carbonaceous chondrite Maribo

We report on the detection of primordial organic matter within the carbonaceous chondrite Maribo that is distinct from the majority of organics found in extraterrestrial samples. We have applied high-spatial resolution techniques to obtain C-N isotopic compositions, chemical, and structural information of this material. The organic matter is depleted in 15N relative to the terrestrial value at around δ15N ~ -200‰, close to compositions in the local interstellar medium. Morphological investigations by electron microscopy revealed that the material consists of µm- to sub-µm-sized diffuse particles dispersed within the meteorite matrix. Electron energy loss and synchrotron X-ray absorption near-edge structure spectroscopies show that the carbon functional chemistry is dominated by aromatic and C=O bonding environments similar to primordial organics from other carbonaceous chondrites. The nitrogen functional chemistry is characterized by C-N double and triple bonding environments distinct from what is usually found in 15N-enriched organics from aqueously altered carbonaceous chondrites. Our investigations demonstrate that Maribo represents one of the least altered CM chondrite breccias found to date and contains primordial organic matter, probably originating in the interstellar medium

Reproducibility of histopathological findings in experimental pathology of the mouse: a sorry tail

Reproducibility of $\textit{in vivo}$ research using the mouse as a model organism depends on many factors, including experimental design, strain or stock, experimental protocols, and methods of data evaluation. Gross and histopathology are often the endpoints of such research and there is increasing concern about the accuracy and reproducibility of diagnoses in the literature. To reproduce histopathological results, the pathology protocol, including necropsy methods and slide preparation, should be followed by interpretation of the slides by a pathologist familiar with reading mouse slides and familiar with the consensus medical nomenclature used in mouse pathology. Likewise, it is important that pathologists are consulted as reviewers of manuscripts where histopathology is a key part of the investigation. The absence of pathology expertise in planning, executing and reviewing $\textit{in vivo}$ research using mice leads to questionable pathology-based findings and conclusions from studies, even in high-impact journals. We discuss the various aspects of this problem, give some examples from the literature and suggest solutions.This work was supported in part by US National Institutes of Health grants R01 AR049288, CA089713 and R21 AR063781 (to J.P.S.) and by The Warden and Fellows of Robinson College, Cambridge (to P.N.S.)

"I try and smile, I try and be cheery, I try not to be pushy. I try to say ‘I’m here for help’ but I leave feeling… worried’’: A qualitative study of perceptions of interactions with health professionals by community-based older adults with chronic pain

Background: Over 50% of community-dwelling older adults experience chronic pain, which threatens their quality of life. Of importance to their pain management is older people’s interaction with health professionals that, if unsatisfactory, may impair the outcome. Aims: To add to the limited research specific to older people living with chronic pain in the community, we explored how they perceive their experiences of interacting with health professionals, seeking factors that might optimise these interactions. Methods: Purposive sampling was used to recruit men and women .65 years with self-reported musculoskeletal chronic pain. Qualitative individual interviews and one group interview were undertaken with 23 participants. Data were transcribed verbatim and underwent Framework Analysis. Results: Three themes were identified. Seeking help illustrates issues around why older people in the community may or may not seek help for chronic pain, and highlights the potential involvement of social comparison. Importance of diagnosis illustrates the desire for professional validation of their condition and an aversion to vague explanations based on the person’s age. Being listened to and being heard illustrates the importance of empathic communication and understanding expectations, with due respect for the person’s age. Conclusions: In common with people of all ages, an effective partnership between an older person in pain and health professionals is essential if pain is to be reported, appropriately assessed and managed, because of the subjective nature of pain and its treatment responses. For older people with pain, perception about their age, by both parties in the partnership, is an additional factor that can unnecessarily interfere with the effectiveness of this partnership. Health professionals should engage with older adults to clarify their expectations about pain and its management, which may be influenced by perceptions about age; and to encourage expression of their concerns, which may also be affected by perceptions about age