Subglacial cetaceans and other mathematical mysteries: a Commentary on “A quantitative test of the thermogenesis hypothesis of cetacean brain evolution,using phylogenetic comparative methods” by C. Maximino

A recent paper published in this Journal purported to provide a quantitative test of the thermogenetic hypothesis of cetacean brain evolution. While using appropriate statistical analyses that account for phylogenetic inertia, errors in the raw data and in interpretation of the thermogenetic hypothesis raise concerns about the validity of the statistical results and the conclusions of the paper. In this commentary the errors in raw data, mathematical approaches, the lack of inclusion of certain data points and misinterpretation of the thermogenetic hypothesis are detailed. The conclusion being that the thermogenetic hypothesis has not been correctly tested by the study.     

Genotypic characterization of Neisseria meningitidis using pyrosequencing™

Pyrosequencing involves the synthesis of single-stranded deoxyribonucleic acid leading to rapid and accurate analysis of nucleotide sequences. This article describes the development of typing assays for the characterization of Neisseria meningitidis using Pyrosequencing. This involved developing methods for the nucleotide sequence analysis of important variable regions contained on a major capsule gene and on outer membrane protein genes that are used for grouping, typing, and subtyping meningococci. To achieve this, primers were designed for amplification of three genes, siaD, porB, and porA from the four main serogroups B, C, Y, and W135. To facilitate throughput and reproducibility, the method was also automated. Data from 717 isolates have shown that Pyrosequencing can be used for the single nucleotide polymorphism and sequence-analysis characterization of meningococci.     

Rapid Assessment of Primer Combinations and Recovery of AFLP™ Products using Ethidium Bromide Staining

AFLP is a novel high-resolution fingerprinting method that can be used to delineate intraspecific relationships among a large variety of fungi and plants. We demonstrate that with the appropriate technical modifications, ethidium bromide staining and non-denaturing polyacryalmide minigels can be an inexpensive and time saving alternative for screening DNA samples for suitable AFLP primer pairs. Furthermore, the recovery of ethidium bromide stained polymorphic DNA fragments is not as tedious as the recovery of isotopic DNA fragments.Abbreviations: EDTA, ethylene diamine tetraacetic acid; BSA, bovine serum albumin.     

Humpback whales interfering when mammal‐eating killer whales attack other species: Mobbing behavior and interspecific altruism?

Humpback whales (Megaptera novaeangliae) are known to interfere with attacking killer whales (Orcinus orca). To investigate why, we reviewed accounts of 115 interactions between them. Humpbacks initiated the majority of interactions (57% vs. 43%; n = 72), although the killer whales were almost exclusively mammal‐eating forms (MEKWs, 95%) vs. fish‐eaters (5%; n = 108). When MEKWs approached humpbacks (n = 27), they attacked 85% of the time and targeted only calves. When humpbacks approached killer whales (n = 41), 93% were MEKWs, and ≥87% of them were attacking or feeding on prey at the time. When humpbacks interacted with attacking MEKWs, 11% of the prey were humpbacks and 89% comprised 10 other species, including three cetaceans, six pinnipeds, and one teleost fish. Approaching humpbacks often harassed attacking MEKWs (≥55% of 56 interactions), regardless of the prey species, which we argue was mobbing behavior. Humpback mobbing sometimes allowed MEKW prey, including nonhumpbacks, to escape. We suggest that humpbacks initially responded to vocalizations of attacking MEKWs without knowing the prey species targeted. Although reciprocity or kin selection might explain communal defense of conspecific calves, there was no apparent benefit to humpbacks continuing to interfere when other species were being attacked. Interspecific altruism, even if unintentional, could not be ruled out.     

Real-time monitoring of PCR amplification of proto-oncogene c-MYC using a Ta₂O₅ electrolyte-insulator-semiconductor sensor

We present a new approach for real-time monitoring of PCR amplification of a specific sequence from the human c-MYC proto-oncogene using a Ta(2)O(5) electrolyte-insulator-semiconductor (EIS) sensor. The response of the fabricated EIS sensor to cycle DNA amplification was evaluated and compared to standard SYBR-green fluorescence incorporation, showing it was possible to detect DNA concentration variations with 30 mV/μM sensitivity. The sensor's response was then optimized to follow in real-time the PCR amplification of c-MYC sequence from a genomic DNA sample attaining an amplification profile comparable to that of a standard real-time PCR. Owing to the small size, ease of fabrication and low-cost, the developed Ta(2)O(5) sensor may be incorporated onto a microfluidic device and then used for real-time PCR. Our approach may circumvent the practical and economical obstacles posed by current platforms that require an external fluorescence detector difficult to miniaturize and incorporate into a lab-on-chip system.     

Record of a new northern range of Sowerby's beaked whale (Mesoplodon bidens )

Two beaked whales identified as Sowerby's beaked whale (Mesoplodon bidens) were observed in sea state 0–1 on 16 July 1995 at 71°30′N 04°00′E in the Norwegian Sea. A number of morphological features, such as dentition, were clearly seen during the encounter. The Sowerby's beaked whale's core distribution is in the North Sea and the previous northernmost sighting was made at 63°06′N 00°41′E. According to the literature, the species has never been recorded in the polar zone. The sighting in the Norwegian Sea suggests that the current data on the species distribution is uncertain, and that its range may include the polar waters of the Norwegian Sea. Received: 24 April 1996 / Accepted: 25 August 1996     

Optimal planning parameters for simultaneous boost IMRT treatment of prostate cancer using a Beam Modulator™

ObjectiveTo determine the optimum energy and beam arrangement for prostate intensity-modulated radiation therapy (IMRT) delivery using an Elekta Beam Modulator? linear accelerator, in order to inform decisions when commissioning IMRT for prostate cancer.MethodsCMS XiO was used to create IMRT plans for a prostate patient. Arrangements with 3, 5, 7, 9 and 11 equally spaced fields, containing both a direct anterior and a direct posterior beam were used, with both 6 MV and 10 MV photons. The effects of varying the maximum number of iterations, leaf increment, number of intensity levels and minimum segment size were investigated. Treatment plans were compared using isodose distributions, conformity indices for targets and critical structures, target dose homogeneity, body dose and plan complexity.ResultsTarget dose conformity and homogeneity and sparing of critical structures improved with an increasing number of beams, although any improvements were small for plans containing more than five fields. Set-ups containing a direct posterior field provided superior conformality around the rectum to anterior beam arrangements. Mean non-target dose and total number of monitor units were higher with 6 MV for all beam arrangements. The dose distribution resulting from seven 6 MV beams was considered clinically equivalent to that with five 10 MV beams.ConclusionMethods have been developed to plan IMRT treatments using XiO for delivery with a Beam Modulator? that fulfil demanding dose criteria, using many different set-ups. This study suggests that 6 MV photons can produce prostate IMRT plans that are comparable to those using 10 MV. Work is ongoing to develop a complete class solution.     

Simultaneous cultivation and disruption of Escherichia coli using glass beads to release recombinant α-amylase and other enzymes

An efficient and reproducible protein recovery procedure from Escherichia coli is presented. Recombinant strains overexpressing recombinant -amylase were cultured in shaken flasks containing small glass beads. Most of the cells underwent mechanical lysis and more than 90% of the -amylase content and also of other non-recombinant enzymes were released into the culture fluid after 24 h. The degree to which the enzymes were released depended on the enzymes and strains involved.     

Proposal of a comprehensive definition of modified and other forms of mycotoxins including “masked” mycotoxins

As the term “masked mycotoxins” encompasses only conjugated mycotoxins generated by plants and no other possible forms of mycotoxins and their modifications, we hereby propose for all these forms a systematic definition consisting of four hierarchic levels. The highest level differentiates the free and unmodified forms of mycotoxins from those being matrix-associated and from those being modified in their chemical structure. The following lower levels further differentiate, in particular, “modified mycotoxins” into “biologically modified” and “chemically modified” with all variations of metabolites of the former and dividing the latter into “thermally formed” and “non-thermally formed” ones. To harmonize future scientific wording and subsequent legislation, we suggest that the term “modified mycotoxins” should be used in the future and the term “masked mycotoxins” to be kept for the fraction of biologically modified mycotoxins that were conjugated by plants.     

Identification of bacteria in blood culture broths using matrix-assisted laser desorption-ionization Sepsityper™ and time of flight mass spectrometry

Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) is a novel method for the direct identification of bacteria from blood culture broths. We evaluate for the first time, the performance of the MALDI Sepsityper? Kit and MS for the identification of bacteria compared to standard phenotypic methods using the manufacturer's specified bacterial identification criteria (spectral scores ≥1.700-1.999 and ≥2.000 indicated identification to genus and species level, respectively). Five hundred and seven positive blood culture broths were prospectively examined, of which 379 (74.8%; 358 monomicrobial, 21 polymicrobial) were identified by MALDI-TOF MS; 195 (100%) and 132 (67.7%) of 195 gram-positive; and 163 (100%) and 149 (91.4%) of 163 gram-negative organisms from monomicrobial blood cultures were correctly identified to genus and species level, respectively. Spectral scores <1.700 (no identification) were obtained in 128/507 (25.2%) positive blood culture broths, including 31.6% and 32.3% of gram-positive and polymicrobial blood cultures, respectively. Significantly more gram-negative organisms were identified compared to gram-positive organisms at species level (p<0.0001). Five blood cultures were misidentified, but at species level only; including four monomicrobial blood cultures with Streptococcus oralis/mitis that were misidentified as Streptococcus pneumoniae. Positive predictive values for the direct identification of both gram-positive and gram-negative bacteria from monomicrobial blood culture broths to genus level were 100%. A diagnostic algorithm for positive blood culture broths that incorporates gram staining and MALDI-TOF MS should identify the majority of pathogens, particularly to genus level.     

Comparative metabolomics of Japanese Black cattle beef and other meats using gas chromatography–mass spectrometry

Progress in metabolomic analysis now allows the evaluation of food quality. This study aims to identify the metabolites in meat from livestock using a metabolomic approach. Using gas chromatography–mass spectrometry (GC/MS), many metabolites were reproducibly detected in meats, and distinct differences between livestock species (cattle, pigs, and chickens) were indicated. A comparison of metabolites between tissues types (muscle, intramuscular fat, and intermuscular fat) in marbled beef of Japanese Black cattle revealed that most metabolites are abundant in the muscle tissue. Several metabolites (medium-chain fatty acids, etc.) involved in triacylglycerol synthesis were uniquely detected in fat tissue. Additionally, the results of multivariate analysis suggest that GC/MS analysis of metabolites can distinguish between cattle breeds. These results provide useful information for the analysis of meat quality using GC/MS-based metabolomic analysis.

ABBREVIATIONS: GC/MS: gas chromatography-mass spectrometry; NMR: nuclear magnetic resonance; MS: mass spectrometry; IS: 2-isopropylmalic acid; MSTFA: N-Methyl-N-trimethylsilyltrifluoroacetamide; CV: coefficient of variation; TBS: Tris-buffered saline; MHC: myosin fast type; PCA: principal component analysis; OPLS-DA: orthogonal partial least-squares discriminant analysis; O2PLS: two-way orthogonal partial least-squares     

Tissue-specific and temporal regulation of a β-conglycinin gene: roles of the RY repeat and other cis-acting elements

Upstream regulatory sequences (URS) of the gene that encodes the subunit of -conglycinin, the 7S soybean seed storage protein, includes two RY repeat elements. The role of RY elements and sequences that bind soybean embryo factors 3 and 4 (SEF3 and SEF4; Allen et al., Plant Cell 1 (1989) 623–631) in regulating expression of the promoter was studied following site directed mutagenesis. Specific mutations introduced into these sequences abolished the in vitro binding activities of SEF3 and SEF4. The biological activities resulting from the mutations were determined in transgenic plants using two chimeric promoters comprising sequences from the CaMV 35S promoter and the subunit promoter. The uidA reporter gene was used to assess the levels of gene expression in transgenic plants. The mutations in the RY element and SEF3 and SEF4 binding sites had little effect on expression of the promoter. By contrast, mutations in the RY element had significant effect on gene expression when the URS from the promoter was ligated upstream of the core 35S promoter. Mutations in the RY element abolished the seed specific enhancing activity of the URS and caused expression of the chimeric promoter in leaves. These results indicate that the RY element plays a key role in seed-specific gene regulation in coordination with other cis-acting elements.     

ζ-Carotene and other carotenes in a Phycomyces mutant

Strain S442, a new mutant of the fungus Phycomyces blakesleeanus, has a greenish colour and a distinct green fluorescence under long-UV light. Carotene analyses reveal the presence of phytoene, ζ-carotene, phytofluene, an unidentified compound, and neurosporene (in descending order of abundance). Genetic analysis shows that the new mutation occurs at gene carB, whose protein product catalyses the four dehydrogenations of phytoene to lycopene via phytofluene, ζ-carotene, and neurosporene. S442 offers no indication of a specific ζ-carotene dehydrogenase. The residual dehydrogenase activity in S442 is inhibited by diphenylamine. The high ζ-carotene content makes S442 a good source of this compound.     

‘Antlers inside’: are the skull structures of beaked whales (Cetacea: Ziphiidae) used for echoic imaging and visual display?

Skulls of many living and extinct beaked whales (Ziphiidae) contain various bizarre bone and tooth structures. Many of them show sexual dimorphism in their skull anatomy: males have bizarre skull structures, whereas females do not. Opinions differ as to what the function of these structures might be. Some believe that these are weapons; others, that they are sound transmitters. This article argues that these structures are the means of visual display. Many of the bizarre bone structures of beaked whales are not exposed like ‘visuals’ of terrestrial tetrapods, but are located deep in soft tissues. Nevertheless, toothed whales recognize objects (including three‐dimensional bodies), using echolocation. So, along with visual means, they can ‘see’ and ‘show’ their internal bone structures with echoic imaging and use them as informational sources in social interactions and in individual or species recognition. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 510–515.     

Diagnosis and therapeutic monitoring of inborn errors of creatine metabolism and transport using liquid chromatography–tandem mass spectrometry in urine,plasma and CSF

Biochemical detection of inborn errors of creatine metabolism or transport relies on the analysis of three main metabolites in biological fluids: guanidinoacetate (GAA), creatine (CT) and creatinine (CTN). Unspecific clinical presentation of the diseases might be the cause that only few patients have been diagnosed so far. We describe a LC–MS/MS method allowing fast and reliable diagnosis by simultaneous quantification of GAA, CT and CTN in urine, plasma and cerebrospinal fluid (CSF) and established reference values for each material.     

Brook lampreys of life: towards holistic monitoring of boreal aquatic habitats using ‘subtle signs’ and oral histories

In this article the observation and spread of brook lamprey (Lampetra planeri) will be discussed as a bio-indicator and a ‘subtle sign’ in the boreal. Brook lamprey is a small non-parasitic freshwater lamprey species indicating good ecological health of aquatic habitats. This article presents knowledge co-produced through a 7-year monitoring programme in the south boreal catchment area of the Jukajoki River, North Karelia, Finland. Over the past one hundred years, this basin has been negatively affected by human land use. Monitoring methods employed as part of this programme have included both rigorous scientific sampling and large-scale traditional and local knowledge (TEK) monitoring. International long-running community monitoring efforts are assessed to position these Finnish traditional knowledge flows. Examples provide for the discussion of new monitoring and restoration methods of boreal aquatic habitats and contribute to the new realisation of these landscapes that were once hidden and now positioned to emerge, providing the suitable social-geographical space is present and accessible to allow for that.     

Evaluation of dose equivalent using a tissue-equivalent ionization chamber and a Geiger-Müller dosimeter

Summary When detailed neutron energy spectrum data are lacking for a mixed field of neutrons and photons, it is permissible when estimating the dose equivalent to assume that the quality factor for the neutrons is 10. With this assumption, it is shown that the responses of a tissue-equivalent ionization chamber and a Geiger-Müller dosimeter can be used to obtain an acceptable approximation of the dose equivalent in the mixed field without requiring precise knowledge of the relative neutron sensitivity of the Geiger-Müller dosimeter.This investigation was supported by Contract EP-78-S-02-4733 from the Department of Energy to the Radiological Research Laboratory/Department of Radiology and by Grant No. CA13696 to the Cancer Center/Institute of Cancer Research, awarded by National Cancer Institute, DHEW     

Reversibility of Vasalgel™ male contraceptive in a rabbit model

Background

Development of a non-hormonal long-acting reversible contraceptive for men could have a significant impact on reducing unintended pregnancies. Vasalgel? is a high molecular weight polymer consisting of styrene-alt-maleic acid (SMA) dissolved in dimethyl sulfoxide being developed as a reversible male contraceptive device. It forms a hydrogel when implanted into the vasa deferentia, which prevents the passage of sperm. Previous studies in the rabbit have proven its efficacy, durability and rapid onset. This study evaluates the capacity to restore sperm concentrations in ejaculates after a reversal procedure.

Methods

Sodium bicarbonate was injected into the vasa deferentia after fourteen months of azoospermia following the injection of two device variations (Vasalgel 100 and Vasalgel 80). Semen samples were then collected for six months and sperm characteristics were compared to baseline levels. Samples of vasa deferentia were obtained for histological examination.

Results

Spermatozoa were present in all subject ejaculates after the reversal procedure. Sperm concentration and sperm motility were similar to baseline levels after reversal, while sperm forward progression was significantly lower and normal acrosomes were not observed. Forward progression percentages increased linearly during six months of semen collection, however, normal acrosomes were not observed at the conclusion of the study. Histologically, several vasa deferentia were clear of the device and contained an intact epithelial lining. A smaller proportion of tissues contained residual test material. A secondary intraluminal inflammatory response was seen occasionally in the tissues containing residual material. There was no difference between the two device variations for studied parameters.

Conclusions

Vasalgel’s prevention of sperm transport for 14 months was reversed through an intravasal injection of sodium bicarbonate. Post-reversal sperm concentrations and motility returned to baseline levels during the six-month follow up. Residual material in the vas lumen or compromised epididymal and vas deferens function may be resulting in reduced forward progression and loss of acrosomes during transit through the vas. Reduced forward progression and the lack of normal acrosomes strongly suggest impaired sperm function.

     

Force predictions relating to tremor and other consequences of a ‘distributed’ model of skeletal muscle

In this brief report, a ‘distributed’ computer model of skeletal muscle is described, and its predictions regarding muscle force and EMG are presented. The force and myo-electric signals are produced as the sum of the contributions of independently activated motor units possessing a distribution of properties. The results of the simulation as well as theoretical study show that: (a) asynchronous activity of motor units can be responsible for the fairly regular oscillations observed in muscle tremor; (b) the use, in the case of muscle, of the limit theorem for the superposition of independent point processes leads to erroneous conclusions with respect to the frequency characteristics of the muscle force waveform, and possibly, with regard to those of the EMG.