The quantitation of buffering action II. Applications of the formal &; general approach

Background  

The paradigm of "buffering" originated in acid-base physiology, but was subsequently extended to other fields and is now used for a wide and diverse set of phenomena. In the preceding article, we have presented a formal and general approach to the quantitation of buffering action. Here, we use that buffering concept for a systematic treatment of selected classical and other buffering phenomena.     

CaCO<Subscript>3</Subscript> supplementation alleviates the inhibition of formic acid on acetone/butanol/ethanol fermentation by <Emphasis Type="Italic">Clostridium acetobutylicum</Emphasis>

Objective

To investigate the inhibiting effect of formic acid on acetone/butanol/ethanol (ABE) fermentation and explain the mechanism of the alleviation in the inhibiting effect under CaCO₃ supplementation condition.

Results

From the medium containing 50 g sugars l^?1 and 0.5 g formic acid l^?1, only 0.75 g ABE l^?1 was produced when pH was adjusted by KOH and fermentation ended prematurely before the transformation from acidogenesis to solventogenesis. In contrast, 11.4 g ABE l^?1 was produced when pH was adjusted by 4 g CaCO₃ l^?1. The beneficial effect can be ascribed to the buffering capacity of CaCO₃. Comparative analysis results showed that the undissociated formic acid concentration and acid production coupled with ATP and NADH was affected by the pH buffering capacity of CaCO₃. Four millimole undissociated formic acid was the threshold at which the transformation to solventogenesis occurred.

Conclusion

The inhibiting effect of formic acid on ABE fermentation can be alleviated by CaCO₃ supplementation due to its buffering capacity.

     

Effects of small <Emphasis Type="Italic">Hsp</Emphasis>genes on developmental stability and microenvironmental canalization

Background  

Progression of development has to be insulated from the damaging impacts of environmental and genetic perturbations to produce highly predictable phenotypes. Molecular chaperones, such as the heat shock proteins (HSPs), are known to buffer various environmental stresses, and are deeply involved in protein homeostasis. These characteristics of HSPs imply that they might affect developmental buffering and canalization.     

Model-based reconstruction of synthetic promoter library in <Emphasis Type="Italic">Corynebacterium glutamicum</Emphasis>

Objective

To develop an efficient synthetic promoter library for fine-tuned expression of target genes in Corynebacterium glutamicum.

Results

A synthetic promoter library for C. glutamicum was developed based on conserved sequences of the ??10 and ??35 regions. The synthetic promoter library covered a wide range of strengths, ranging from 1 to 193% of the tac promoter. 68 promoters were selected and sequenced for correlation analysis between promoter sequence and strength with a statistical model. A new promoter library was further reconstructed with improved promoter strength and coverage based on the results of correlation analysis. Tandem promoter P70 was finally constructed with increased strength by 121% over the tac promoter. The promoter library developed in this study showed a great potential for applications in metabolic engineering and synthetic biology for the optimization of metabolic networks.

Conclusions

To the best of our knowledge, this is the first reconstruction of synthetic promoter library based on statistical analysis of C. glutamicum.

     

Construction and transformation of a <Emphasis Type="Italic">Thermotoga-E. coli</Emphasis>shuttle vector

Background  

Thermotoga spp. are attractive candidates for producing biohydrogen, green chemicals, and thermostable enzymes. They may also serve as model systems for understanding life sustainability under hyperthermophilic conditions. A lack of genetic tools has hampered the investigation and application of these organisms. This study aims to develop a genetic transfer system for Thermotoga spp.     

The high intracellular ph buffering of hagfish (Eptatretus cirrhatus) dental plate retractor muscle cannot be attributed to the known histidine-related compounds present in other vertebrates

• 1.1. Intracellular pH buffering capacity of hagfish (Eplatretus cirrhatus) dental plate retractor muscles is among the highest reported for any vertebrate muscle.
• 2.2. Over 80% of the pH buffering capacity of hagfish retractor and myotome muscle is due to components other than proteins and phosphate.
• 3.3. The muscles have less than 0.5 μmol/g wet weight of l-histidine, and lack l-l-methyl histidine, l-3-methyl histidine and the histidine-containing dipeptides anserine, carnosine and ophidine.
• 4.4. Instead, they contain an unidentified low molecular weight acid-soluble compound to which the high pH buffering capacity can be attributed.

     

Calibrating E-values for MS2 database search methods

Background  

The key to mass-spectrometry-based proteomics is peptide identification, which relies on software analysis of tandem mass spectra. Although each search engine has its strength, combining the strengths of various search engines is not yet realizable largely due to the lack of a unified statistical framework that is applicable to any method.     

Modelling the acid/base <Superscript>1</Superscript>H NMR chemical shift limits of metabolites in human urine

Introduction

Despite the use of buffering agents the ¹H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples.

Objectives

To investigate the acid, base and metal ion dependent ¹H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture.

Methods

Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl₂, MgCl₂, NaCl or KCl, and their ¹H NMR spectra were acquired.

Results

Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na⁺, K⁺, Ca²⁺ and Mg²⁺, were also measured.

Conclusion

These data will be a valuable resource for ¹H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for ¹H NMR spectra.

     

Old‐growth forests buffer climate‐sensitive bird populations from warming

Aim

Habitat loss and climate change constitute two of the greatest threats to biodiversity worldwide, and theory predicts that these factors may act synergistically to affect population trajectories. Recent evidence indicates that structurally complex old‐growth forest can be cooler than other forest types during spring and summer months, thereby offering potential to buffer populations from negative effects of warming. Old growth may also have higher food and nest‐site availability for certain species, which could have disproportionate fitness benefits as species approach their thermal limits.

Location

Pacific Northwestern United States.

Methods

We predicted that negative effects of climate change on 30‐year population trends of old‐growth‐associated birds should be dampened in landscapes with high proportions of old‐growth forest. We modelled population trends from Breeding Bird Survey data for 13 species as a function of temperature change and proportion old‐growth forest.

Results

We found a significant negative effect of summer warming on only two species. However, in both of these species, this relationship between warming and population decline was not only reduced but reversed, in old‐growth‐dominated landscapes. Across all 13 species, evidence for a buffering effect of old‐growth forest increased with the degree to which species were negatively influenced by summer warming.

Main conclusions

These findings suggest that old‐growth forests may buffer the negative effects of climate change for those species that are most sensitive to temperature increases. Our study highlights a mechanism whereby management strategies to curb degradation and loss of old‐growth forests—in addition to protecting habitat—could enhance biodiversity persistence in the face of climate warming.

     

Resistance Training Reduces Skeletal Muscle Work Efficiency in Weight‐Reduced and Non–Weight‐Reduced Subjects

Objective

The objective of this study is to determine whether resistance training is similarly effective in reducing skeletal muscle efficiency and increasing strength in weight‐reduced and maximal weight subjects.

Methods

This study examined the effects of supervised resistance exercise on skeletal muscle in 14 individuals with overweight and obesity sustaining a 10% or greater weight loss for over 6 months and a phenotypically similar group of 15 subjects who had not reduced weight and were weight stable at their maximal lifetime body weight. We assessed skeletal muscle work efficiency and fuel utilization (bicycle ergometry), strength (dynamometry), body composition (dual energy x‐ray absorptiometry), and resting energy expenditure (indirect calorimetry) before and after 12 weeks of thrice‐weekly resistance training.

Results

Non–weight‐reduced subjects were significantly (10%‐20%) stronger before and after the intervention than reduced‐weight subjects and gained significantly more fat‐free mass with a greater decline in percentage of body fat than weight‐reduced subjects. Resistance training resulted in similar significant decreases (~10%) in skeletal muscle work efficiency at low‐level exercise and ~10% to 20% increases in leg strength in both weight‐reduced and non–weight‐reduced subjects.

Conclusions

Resistance training similarly increases muscle strength and decreases efficiency regardless of weight loss history. Increased resistance training could be an effective adjunct to reduced‐weight maintenance therapy.

     

Origin of tendon stem cells <Emphasis Type="Italic">in situ</Emphasis>

Background

Adult stem cells are surveillance repositories capable of supplying a renewable source of progenitors for tissue repair and regeneration to maintain tissue homeostasis throughout life. Many tissue-resident stem cells have been identified in situ, which lays the foundation for studying them in their native microenvironment, i.e. the niche. Within the musculoskeletal system, muscle stem cells have been unequivocally identified in the mouse, which have led to considerable advances in understanding their role in muscle homeostasis and regeneration. On the other hand, for bone and tendon progenitor cells, mesenchymal stem cells have been used as the main in vitro cell model as they can differentiate into osteogenic, chondrogenic and tenogenic fates. Despite considerable efforts and employment of modern tools, the in vivo origins of bone and tendon stem cells remain debated. Tendon regeneration via stem cells is understudied and deserves attention as tendon damage is noted for a bleak, time-consuming recovery and the repaired tendon seldom regains the structural integrity and strength of the native, uninjured state.

Objective

Here we review the past efforts and recent studies toward defining adult tendon stem cells and understanding tendon regeneration instead of tendon development. The focus is on adult tendon resident cells in situ and the uncertainty of their roles in regeneration.

Methods

A systematic literature search using the Pubmed search engine was conducted encompassing the seminal papers in the tendon field.

Conclusion

Investigation of tendon stem cells in situ is in its infancy mainly due to lack of necessary tools and standardized injury model. We propose a concerted effort toward establishing a comprehensive cell atlas of the tendon, making genetic tools and choosing a reliable injury model for coordinated studies among different laboratories. Increasing our basic understanding should aid future therapeutic innovations to shorten and enhance the tendon repair/regeneration process.

     

Fine root traits in <Emphasis Type="Italic">Chamaecyparis obtusa</Emphasis> forest soils with different acid buffering capacities

Key message

The biomass, morphology, and respiration of the fine roots of Chamaecyparis obtusa did not change between different soil acid buffering capacities. Soil nitrate has noticeable effects on morphology and respiration.

Abstract

Low soil acid buffering capacity (ABC) accelerates soil acidification because of the lower concentrations of base cations (BC) and higher concentrations of aluminum (Al) present under such conditions. More information on fine root traits across soil ABC gradients is required to evaluate the effects of accelerated soil acidification in mature forests, especially in East Asia. We investigated the biomass, morphology (specific root length; SRL), and respiration rates of fine roots and analyzed the soil nitrogen status in seven Chamaecyparis obtusa stands with two highly contrasting ABC soils. There were no significant differences in the biomass, SRL, and respiration rates of fine roots between high- and low-ABC stands. However, fine roots in the low-ABC stands were concentrated in the uppermost soil layers and the biomass proportion of roots <0.5 mm in diameter was higher in low-ABC stands than in high-ABC stands. The fine root biomass increased with increasing soil Al, NH₄ ⁺-N, and C and with decreasing soil BC and bulk density. The SRL and respiration rates of fine roots were positively correlated with soil NO₃ ^?-N. We conclude that the fine root traits were affected not only by soil ABC but also by other soil properties in the forest.

     

Some statistical properties of regulatory DNA sequences,and their use in predicting regulatory regions in the <Emphasis Type="Italic">Drosophila</Emphasis> genome: the fluffy-tail test

Background  

This paper addresses the problem of recognising DNA cis-regulatory modules which are located far from genes. Experimental procedures for this are slow and costly, and computational methods are hard, because they lack positional information.     

Parasexual genetics of <Emphasis Type="Italic">Dictyostelium</Emphasis> gene disruptions: identification of a ras pathway using diploids

Background  

The relative ease of targeted gene disruption in the social amoeba Dictyostelium has stimulated its widespread use as an experimental organism for cell and developmental biology. However, the field has been hamstrung by the lack of techniques to recombine disrupted genes.     

PKQuest: volatile solutes – application to enflurane, nitrous oxide, halothane, methoxyflurane and toluene pharmacokinetics

Background  

The application of physiologically based pharmacokinetic models (PBPK) to human studies has been limited by the lack of the detailed organ information that is required for this analysis. PKQuest is a new generic PBPK that is designed to avoid this problem by using a set of "standard human" default parameters that are applicable to most solutes.     

OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data

Background  

Today, data evaluation has become a bottleneck in chromatographic science. Analytical instruments equipped with automated samplers yield large amounts of measurement data, which needs to be verified and analyzed. Since nearly every GC/MS instrument vendor offers its own data format and software tools, the consequences are problems with data exchange and a lack of comparability between the analytical results. To challenge this situation a number of either commercial or non-profit software applications have been developed. These applications provide functionalities to import and analyze several data formats but have shortcomings in terms of the transparency of the implemented analytical algorithms and/or are restricted to a specific computer platform.     

<Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> interactome analysis unravels potential pathways to drug resistance

Background  

Emergence of drug resistant varieties of tuberculosis is posing a major threat to global tuberculosis eradication programmes. Although several approaches have been explored to counter resistance, there has been limited success due to a lack of understanding of how resistance emerges in bacteria upon drug treatment. A systems level analysis of the proteins involved is essential to gain insights into the routes required for emergence of drug resistance.