Exploring the bovine rumen bacterial community from birth to adulthood

The mammalian gut microbiota is essential in shaping many of its host''s functional attributes. One such microbiota resides in the bovine digestive tract in a compartment termed as the rumen. The rumen microbiota is necessary for the proper physiological development of the rumen and for the animal''s ability to digest and convert plant mass into food products, making it highly significant to humans. The establishment of this microbial population and the changes occurring with the host''s age are important for understanding this key microbial community. Despite its importance, little information about colonization of the microbial populations in newborn animals, and the gradual changes occurring thereafter, exists. Here, we characterized the overall bovine ruminal bacterial populations of five age groups, from 1-day-old calves to 2-year-old cows. We describe the changes occurring in the rumen ecosystem after birth, reflected by a decline in aerobic and facultative anaerobic taxa and an increase in anaerobic ones. Some rumen bacteria that are essential for mature rumen function could be detected as early as 1 day after birth, long before the rumen is active or even before ingestion of plant material occurs. The diversity and within-group similarity increased with age, suggesting a more diverse but homogeneous and specific mature community, compared with the more heterogeneous and less diverse primary community. In addition, a convergence toward a mature bacterial arrangement with age was observed. These findings have also been reported for human gut microbiota, suggesting that similar forces drive the establishment of gut microbiotas in these two distinct mammalian digestive systems.     

Quantitative Analysis of Protein Expression to Study Lineage Specification in Mouse Preimplantation Embryos

This protocol presents a method to perform quantitative, single-cell in situ analyses of protein expression to study lineage specificationin mouse preimplantation embryos. The procedures necessary for embryo collection, immunofluorescence, imaging on a confocal microscope, and image segmentation and analysis are described. This method allows quantitation of the expression of multiple nuclear markers and the spatial (XYZ) coordinates of all cells in the embryo. It takes advantage of MINS, an image segmentation software tool specifically developed for the analysis of confocal images of preimplantation embryos and embryonic stem cell (ESC) colonies. MINS carries out unsupervised nuclear segmentation across the X, Y and Z dimensions, and produces information on cell position in three-dimensional space, as well as nuclear fluorescence levels for all channels with minimal user input. While this protocol has been optimized for the analysis of images of preimplantation stage mouse embryos, it can easily be adapted to the analysis of any other samples exhibiting a good signal-to-noise ratio and where high nuclear density poses a hurdle to image segmentation (e.g., expression analysis of embryonic stem cell (ESC) colonies, differentiating cells in culture, embryos of other species or stages, etc.).     

Molecular genetic improvements of cyanobacteria to enhance the industrial potential of the microbe: A review

The rapid increase in worldwide population coupled with the increasing demand for fossil fuels has led to an increased urgency to develop sustainable sources of energy and chemicals from renewable resources. Using microorganisms to produce high‐value chemicals and next‐generation biofuels is one sustainable option and is the focus of much current research. Cyanobacteria are ideal platform organisms for chemical and biofuel production because they can be genetically engineered to produce a broad range of products directly from CO₂, H₂O, and sunlight, and require minimal nutrient inputs. The purpose of this review is to provide an overview on advances that have been or could be made to improve strains of cyanobacteria for industrial purposes. First, the benefits of using cyanobacteria as a platform for chemical and biofuel production are discussed. Next, an overview of cyanobacterial strain improvements by genetic engineering is provided. Finally, mutagenesis techniques to improve the industrial potential of cyanobacteria are described. Along with providing an overview on various areas of research that are currently being investigated to improve the industrial potential of cyanobacteria, this review aims to elucidate potential targets for future research involving cyanobacteria as an industrial microorganism. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1357–1371, 2016     

The effect of two cryopreservation methods on human sperm DNA damage

Several methods are currently available for selection when conducting sperm cryopreservation, however, these methods might cause different degrees of damage on sperm DNA. The aim of the this study is to compare the effects of storage at −80 °C (in ultra-low temperature refrigerator) and at −196 °C (in liquid nitrogen) on sperm DNA damage, thus to provide a reference for choosing the right method according to different aims. We randomly collected 28 semen samples from college students of Chongqing city. The samples stored at −80 °C were neat semen samples and the samples stored at −196 °C were mixed with additional cryoprotectants. Each sample was subjected to two freezing-thawing cycles, and the sperm DNA damage levels of fresh and thawed samples were measured by single cell gel electrophoresis (SCGE) and sperm chromatin structure assay (SCSA). Both SCGE and SCSA assays showed cryopreservation induced significant damage to sperm DNA. However, storage at −196 °C lead to more severe damage to sperm DNA than storage at −80 °C measured by SCSA. Sperm DNA damage increased simultaneously with the higher frequency of freezing-thawing cycles. We concluded that storage of neat semen samples at −80 °C had milder damage to sperm DNA than storage at −196 °C mixed with cryoprotectants. To avoid additional sperm DNA damage, repeated freezing and thawing should be prevented.     

Mesophilic Mineral-Weathering Bacteria Inhabit the Critical-Zone of a Perennially Cold Basaltic Environment

The weathering of silicate in the world's critical-zone (rock-soil interface) is a natural mechanism providing a feedback on atmospheric CO₂ concentrations through the carbonate-silicate cycle. We examined culturable bacterial communities from a critical-zone in western Iceland to determine the optimum growth temperature and their ability to solubilize phosphate-containing minerals, which are abundant within the critical-zone area examined here. The majority of isolated bacteria were able to solubilize mineral-state phosphate. Almost all bacterial isolates were mesophilic (growth optima of 20–45°C), despite critical-zone temperatures that were continuously below 15°C, although all isolates could grow at temperatures associated with the critical-zone (?2.8–13.1°C). Only three isolates were shown to have thermal optima for growth that were within temperatures experienced at the critical-zone. These findings show that the bacteria that inhabit the western Icelandic critical-zone have temperature growth optima suboptimally adapted to their environment, implying that other adaptations may be more important for their long-term persistance in this environment. Moreover, our study showed that the cold basaltic critical-zone is a region of active phosphate mineral-weathering.     

Mass spectrometry applications in microbiology beyond microbe identification: progress and potential

Introduction: Mass spectrometry (MS), particularly MALDI-time of flight (MALDI-TOF), has become a routine tool for microorganism identification in clinical microbiology laboratories in the last five years. The use of MALDI-TOF MS has accelerated laboratory analysis, thus providing accurate species-level information with very short turnaround times.

Areas covered: Beyond microbe identification, MALDI-TOF MS offers great opportunities for fast strain typing and detection of antimicrobial susceptibility/resistance in both bacterial and fungal organisms. Drawing on evidence from PubMed literature searches, clinical microbiology laboratory experience, and the authors’ opinions, this review summarizes recent significant advances and ongoing challenges in these areas.

Expert commentary: In the near future, it is expected that the implementation of new analytical algorithms, automation of procedures, and refinement of assays will enhance the clinical and epidemiological usefulness of MALDI-TOF and other MS technologies.     

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

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Population and Single-Cell Analysis of Human Cardiogenesis Reveals Unique LGR5 Ventricular Progenitors in Embryonic Outflow Tract

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