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Robust sampling and preservation of DNA for microbial community profiling in field experiments | BMC Research Notes | Full Text

Robust sampling and preservation of DNA for microbial community profiling in field experiments | BMC Research Notes | Full Text

BMC Research Notes

Robust sampling and preservation of DNA for microbial community profiling in field experiments

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BMC Research Notes201912:159
  • Received: 30 January 2019
  • Accepted: 13 March 2019
  • Published: 

Abstract

Objective

Stabilising samples of microbial communities for DNA extraction without access to laboratory equipment can be a challenging task. In this paper we propose a method using filter paper disks for the preservation of DNA from diverse microbial communities which are found in a fermented milk product.

Results

Small adaptations to the DNA extraction method used for liquid fermented milk delivered DNA of sufficient amounts and quality to be used for later analyses, e.g. full community 16S amplicon sequencing. The microbial community structure obtained via the filter paper method showed sufficient resemblance to the structure obtain via the traditional DNA extraction from the liquid milk sample. This method can therefore successfully be used to analyse diverse microbial communities from fermented milk products from remote areas.

Keywords

  • Filter paper disks
  • Field trial
  • Microbial community
  • Milk
  • Fermentation
  • DNA stabilisation

Impairment of tissue repair in pneumonia due to β-cell deficiency: role of endoplasmic reticulum stress in alveolar macrophages | BMC Research Notes | Full Text

Impairment of tissue repair in pneumonia due to β-cell deficiency: role of endoplasmic reticulum stress in alveolar macrophages | BMC Research Notes | Full Text

BMC Research Notes

Impairment of tissue repair in pneumonia due to β-cell deficiency: role of endoplasmic reticulum stress in alveolar macrophages

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  • Email author and
BMC Research Notes201912:160
  • Received: 22 October 2018
  • Accepted: 18 March 2019
  • Published: 

Abstract

Objective

Diabetes mellitus (DM) patients are susceptible to delayed resolution of pneumonia. However, the pathogenesis of the impaired tissue repair in inflamed lungs in diabetic patients is unknown. We evaluated phagocytosis of apoptotic cells (efferocytosis), hepatocyte growth factor (HGF) production in bronchoalveolar lavage fluid (BALF), and lung histology in the resolution phase following acute lung injury in streptozotocin (STZ)-induced β-cell-depleted hyperglycemic mice. We also investigated efferocytosis and HGF production by macrophages under β-cell depletion condition ex vivo.

Results

In β-cell-depleted mice, efferocytosis was not significantly different from that in control mice; however, the concentration of HGF in BALF was decreased. In addition, diminished HGF production by alveolar macrophages and DNA synthesis in the alveolar epithelium was observed by immunohistochemistry. Ex vivo experiments confirmed that HGF production by macrophages was impaired under β-cell depletion probably because of endoplasmic reticulum stress.

Keywords

  • Diabetes mellitus
  • Pneumonia
  • Hepatocyte growth factor
  • Endoplasmic reticulum stress

Prevalence and associated factors of unintended pregnancy among pregnant woman in Gondar town, North west Ethiopia, 2014 | BMC Research Notes | Full Text

Prevalence and associated factors of unintended pregnancy among pregnant woman in Gondar town, North west Ethiopia, 2014 | BMC Research Notes | Full Text

BMC Research Notes

Prevalence and associated factors of unintended pregnancy among pregnant woman in Gondar town, North west Ethiopia, 2014

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Contributed equally
BMC Research Notes201912:161
  • Received: 12 January 2019
  • Accepted: 16 March 2019
  • Published: 

Abstract

Objective

The purpose of this study was to assess prevalence and associated factors of unintended pregnancy among pregnant women in Gondar town, North western Ethiopia, 2014. A community based cross-sectional study was conducted among pregnant women to select 325 participants for face to face interview by using simple random sampling technique from April 1–May 30, 2014. Bivariate and multivariate data analysis was performed using SPSS for Windows version 20 and level of significance of association was determined at P value < 0.05.

Result

This study identified that 20.6% of pregnant women were unintended of which 6.8 were mistimed and 13.8 were unwanted. Unintended pregnancy was associated with family size (≥ 4) (AOR = 2.92; 95% CI 1.605, 5.31), marital status (single) (AOR = 12.59; 95% CI 5.18, 30.6) and age at first pregnancy < 18 years AOR (95% CI) 3.02 (1.522, 6.245). Therefore it is important to adequately counsel women concerning positive mind-sets about its prevention mechanism and its consequences of unintended pregnancies.

Keywords

  • Unintended
  • Pregnancy
  • Gondar town

Development and use of a flexible data harmonization platform to facilitate the harmonization of individual patient data for meta-analyses | BMC Research Notes | Full Text

Development and use of a flexible data harmonization platform to facilitate the harmonization of individual patient data for meta-analyses | BMC Research Notes | Full Text



BMC Research Notes

Development and use of a flexible data harmonization platform to facilitate the harmonization of individual patient data for meta-analyses

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  • ,
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BMC Research Notes201912:164
  • Received: 25 October 2018
  • Accepted: 18 March 2019
  • Published: 

Abstract

Objective

Harmonizing individual patient data (IPD) for meta-analysis has clinical and statistical advantages. Harmonizing IPD from multiple studies may benefit from a flexible data harmonization platform (DHP) that allows harmonization of IPD already during data collection. This paper describes the development and use of a flexible DHP that was initially developed for the Predicting OptimaL cAncer RehabIlitation and Supportive care (POLARIS) study.

Results

The DHP that we developed (I) allows IPD harmonization with a flexible approach, (II) has the ability to store data in a centralized and secured database server with large capacity, (III) is transparent and easy in use, and (IV) has the ability to export harmonized IPD and corresponding data dictionary to a statistical program. The DHP uses Microsoft Access as front-end application and requires a relational database management system such as Microsoft Structured Query Language (SQL) Server or MySQL as back-end application. The DHP consists of five user friendly interfaces which support the user to import original study data, to harmonize the data with a master data dictionary, and to export the harmonized data into a statistical software program of choice for further analyses. The DHP is now also adopted in two other studies.

Keywords

  • Flexible data harmonization platform
  • Easy in use infrastructure
  • Centralized and secured database server

Comparing DNA quantity and quality using saliva collection following food and beverage consumption | BMC Research Notes | Full Text

Comparing DNA quantity and quality using saliva collection following food and beverage consumption | BMC Research Notes | Full Text



BMC Research Notes

Comparing DNA quantity and quality using saliva collection following food and beverage consumption

BMC Research Notes201912:165
  • Received: 3 January 2019
  • Accepted: 18 March 2019
  • Published: 

Abstract

Objective

With the democratization of genetic testing, researchers, clinicians, and educators must consider the varying degree of field conditions when collecting samples for genetic analyses. For genotyping or sequencing studies, study designers have multiple options from which to choose, including cheek swabs and saliva sampling. One significant benefit of saliva collection is that it can be done remotely, in the privacy of one’s home. This same benefit adds a risk of compliance. Therefore, our goal with this study was to see if the quality and quantity of the saliva collection by a saliva DNA collection kit would be affected by not following the manufacturer’s directions, i.e., drinking or eating right before collection.

Results

We asked five participants to collect saliva samples according to the manufacturer’s guidance and also after consuming five food items or beverages. We evaluated DNA quantity and quality post-purification using spectroscopy, electrophoresis, and polymerase chain reaction genotyping. Consistent with our hypothesis, we did not see a difference in quantity or quality of the isolated DNA. From our results, we conclude that the manufacturer’s instructions serve as an ideal guideline, but the collection devices are robust enough to permit flexibility in sampling at home or in the field.

Keywords

  • Saliva sampling
  • DNA collection methods
  • Non-invasive sampling
  • Genetic methods

Effect of lesion proximity on the regenerative response of long descending propriospinal neurons after spinal transection injury | BMC Neuroscience | Full Text

Effect of lesion proximity on the regenerative response of long descending propriospinal neurons after spinal transection injury | BMC Neuroscience | Full Text

BMC Neuroscience

Effect of lesion proximity on the regenerative response of long descending propriospinal neurons after spinal transection injury

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Contributed equally
BMC Neuroscience201920:10
  • Received: 25 May 2018
  • Accepted: 5 March 2019
  • Published: 

Abstract

Background

The spinal cord is limited in its capacity to repair after damage caused by injury or disease. However, propriospinal (PS) neurons in the spinal cord have demonstrated a propensity for axonal regeneration after spinal cord injury. They can regrow and extend axonal projections to re-establish connections across a spinal lesion. We have previously reported differential reactions of two distinct PS neuronal populations—short thoracic propriospinal (TPS) and long descending propriospinal tract (LDPT) neurons—following a low thoracic (T10) spinal cord injury in a rat model. Immediately after injury, TPS neurons undergo a strong initial regenerative response, defined by the upregulation of transcripts to several growth factor receptors, and growth associated proteins. Many also initiate a strong apoptotic response, leading to cell death. LDPT neurons, on the other hand, show neither a regenerative nor an apoptotic response. They show either a lowered expression or no change in genes for a variety of growth associated proteins, and these neurons survive for at least 2 months post-axotomy. There are several potential explanations for this lack of cellular response for LDPT neurons, one of which is the distance of the LDPT cell body from the T10 lesion. In this study, we examined the molecular response of LDPT neurons to axotomy caused by a proximal spinal cord lesion.

Results

Utilizing laser capture microdissection and RNA quantification with branched DNA technology, we analyzed the change in gene expression in LDPT neurons following axotomy near their cell body. Expression patterns of 34 genes selected for their robust responses in TPS neurons were analyzed 3 days following a T2spinal lesion. Our results show that after axonal injury nearer their cell bodies, there was a differential response of the same set of genes evaluated previously in TPS neurons after proximal axotomy, and LDPT neurons after distal axotomy (T10spinal transection). The genetic response was much less robust than for TPS neurons after proximal axotomy, included both increased and decreased expression of certain genes, and did not suggest either a major regenerative or apoptotic response within the population of genes examined.

Conclusions

The data collectively demonstrate that the location of axotomy in relation to the soma of a neuron has a major effect on its ability to mount a regenerative response. However, the data also suggest that there are endogenous differences in the LDPT and TPS neuronal populations that affect their response to axotomy. These phenotypic differences may indicate that different or multiple therapies may be needed following spinal cord injury to stimulate maximal regeneration of all PS axons.

Keywords

  • Propriospinal neurons
  • Spinal cord injury
  • Axonal regeneration
  • Gene expression
  • Axotomy location
  • Intrinsic response