Personalized medicine and proteomics: lessons from non-small cell lung cancer

Personalized medicine allows the selection of treatments best suited to an individual patient and disease phenotype. To implement personalized medicine, effective tests predictive of response to treatment or susceptibility to adverse events are needed, and to develop a personalized medicine test, both high quality samples and reliable data are required. We review key features of state-of-the-art proteomic profiling and introduce further analytic developments to build a proteomic toolkit for use in personalized medicine approaches. The combination of novel analytical approaches in proteomic data generation, alignment and comparison permit translation of identified biomarkers into practical assays. We further propose an expanded statistical analysis to understand the sources of variability between individuals in terms of both protein expression and clinical variables and utilize this understanding in a predictive test.     

Study of amino acid formation during palmitate oxidation in rat brain mitochondria

The interrelation of palmitate oxidation with amino acid formation in rat brain mitochondria has been investigated in purified mitochondria of nonsynaptic origin by measuring the formation of aspartate, -ketoglutarate, and glutamate during palmitate oxidation, and also by assaying¹⁴C-products of [1-¹⁴C]palmitate oxidation. Oxidation of palmitate (or [1-¹⁴C]palmitate) resulted in the formation of aspartate (or¹⁴C-aspartate), and the oxidation was inhibited by aminooxyacetate (an inhibitor of transaminase), Palmitate oxidation also resulted in -ketoglutarate formation, which was sensitive to the effect of aminooxyacetate. Addition of NH₄Cl was found to increase¹⁴C-products and formation of -ketoglutarate, whereas glutamate formation was not increased unless the rate of palmitate oxidation was reduced by 50% by aminooxyacetate or -ketoglutarate was added exogenously. Exogenous -ketoglutarate was found to decrease¹⁴C-products, but not aspartate formation. These results indicated that palmitate oxidation was closely related to aspartate formation via aspartate aminotransferase. During palmitate oxidation without aminooxyacetate or added -ketoglutarate, however, -ketoglutarate was not available for glutamate formation via glutamate dehydrogenase. We discuss the possibility that this was because (a) oxidative decarboxylation of -ketoglutarate to form succinyl-CoA was favored over glutamate formation for the competition for -ketoglutarate in the same pool, and (b) the pool of -ketoglutarate produced in the aspartate aminotransferase reaction did not serve as substrate for glutamate formation.     

Effects of Silicon-Limitation on Growth and Morphology of Triparma laevis NIES-2565 (Parmales,Heterokontophyta)

The order Parmales (Heterokontophyta) is a group of small-sized unicellular marine phytoplankton, which is distributed widely from tropical to polar waters. The cells of Parmales are surrounded by a distinctive cell wall, which consists of several siliceous plates fitting edge to edge. Phylogenetic and morphological analyses suggest that Parmales is one of the key organisms for elucidating the evolutionary origin of Bacillariophyceae (diatoms), the most successful heterokontophyta. The effects of silicon-limitation on growth and morphogenesis of plates were studied using a strain of Triparma laevis NIES-2565, which was cultured for the first time in artificial sea water. The cells of T. laevis were surrounded by eight plates when grown with sufficient silicon. However, plate formation became incomplete when cells were cultured in a medium containing low silicate (ca. <10 µM). Cells finally lost almost all plates in a medium containing silicate concentrations lower than ca. 1 µM. However, silicon-limitation did not affect growth rate; cells continued to divide without changing their growth rate, even after all plates were lost. Loss of plates was reversible; when cells without plates were transferred to a medium containing sufficient silicate, regeneration of shield and ventral plates was followed by the formation of girdle and triradiate plates. The results indicate that the response to silicon-limitation of T. laevis is different from that of diatoms, where cell division becomes inhibited under such conditions.     

Masculinization mechanism of hybrids in bitterlings (Teleostei: Cyprinidae)

The sex ratio of bitterling hybrids (subfamily: Acheilognathinae) is often likely to be biased toward males. Artificial hybridization was carried out in 10 species of bitterlings (three genera) in order to elucidate the masculinization mechanism of hybrids. Tanakia himantegus never produced viable F1 hybrids with other species, while hybrids of most other species were viable. In terms of sex ratio and fertility, hybrids were clearly divided into two groups: congeneric Tanakia hybrids and others. Both male and female congeneric Tanakia hybrids were fertile. The sex ratio was nearly 1:1 in all groups of Tanakia hybrids. Except for the congeneric Tanakia hybrids, sterile males appeared predominantly in groups of hybrids in which females were very rare but remained fertile. Sterile intersexes were also observed in five hybrid groups: T. lanceolata (female) x Acheilognathus cyanostigma (male), Rhodeus uyekii (female) x T. lanceolata (male), A. rhombeus (female) x T. lanceolata (male), A. rhombeus (female) x T. limbata (male), and A. tabira tabira (female) x A. cyanostigma (male). In the development of male-predominant hybrids, although hybrid and control (parental species) hatching and survival rates do not differ, no females appeared in hybrids, contrary to the controls. Taking the female heterogametic sex-determining system (ZW) and the phylogenetic relationship of bitterlings into consideration, the masculinization mechanism of hybrids in bitterlings can be explained by the interaction of two sex chromosomes, derived from each parental species. The basic genetic sex in bitterlings is male (ZZ) and the derivative is female (ZW). When parental species are related, the sex phenotype of hybrids coincides with the genetic sex. However, when the parental species differ, the sex phenotype of the ZW genotype is reversed to become male by an abnormal interaction between the Z and W chromosomes. The rare appearance of females and intersexes in male-predominant hybrids might be due to complete or partial functional expression of the W chromosome.     

Chryseobacterium miricola sp. nov., a novel species isolated from condensation water of space station Mir

Classification of strain W3-B1, which was isolated from condensation water in the Russian space laboratory Mir, was investigated by a polyphasic taxonomic approach. Cells of strain W3-B1 were nonmotile, asporogenous, gram-negative slender rods with rounded ends. 16S rRNA gene sequence analysis indicated that organism should be placed in the genus Chryseobacterium. This organism contains menaquinone MK-6 as the predominent isoprenoid quinone and 3-OH iso 17:0 (40%), iso 15:0 (33%) as the major fatty acids. Phylogenetically, the nearest relative of strain W3-B1 is Chryseobacterium meningosepticum with sequence similarity of 98.4%, but DNA-DNA hybridization resulted in similarity values of only 52.3%. The G+C mol% is 34.6 mol%. Based upon results obtained by morphological, biochemical, chemotaxonomic, and molecular methods, strain W3-B1 was clearly distinguishable from other Chryseobacterium species. For these reasons, a novel species of family Flavobacteriaceae is proposed; strain W3-B1(T) (= GTC 862(T) = JCM 11413(T) = DSM 14571(T)) is the type strain.     

Stress relaxation properties of the cell wall of tissue segments under different growth conditions

Stress-relaxation parameters were compared under different experimentalconditions using 5th internode segments of light-grown pea seedlingsand coleoptile segments of dark-grown Avena seedlings. The followingresults were obtained. 1. In a short incubation period at 25?C, IAA caused a decreasein the minimum relaxation time, To, of the epidermal cell wallof pea internodes when it induced elongation; the optimum concentrationof IAA for decreasing To was 10 mg/liter. 2. At all concentrations of IAA used, 0.1–1000 mg/liter,the relationship between the To value of the epidermal cellwall peeled from segments incubated for 2 hr and the subsequentelongation rate in 2–3 hr incubation was linear, indicatingthat the To value of the cell wall at a certain time regulatesthe rate of the following elongation. 3. When segments of pea epicotyls or Avena coleoptiles wereincubated in mannitol solution of various concentrations inthe presence and absence of IAA and then allowed to grow inthe absence of both mannitol and IAA, the segments extendeddifferently depending upon the mannitol concentration, whichwas less than 0.3 M, given during preincubation. 4. The T_o and b (relaxation rate, S/log t) values were smallerin the cell wall of segments which extended more, than in thosewhich extended less. In this case, 0.2 M mannitol solution wasmost effective, since it inhibited IAA-induced elongation duringpre-incubation and the segments thus incubated extended themost afterward. 5. Extensibility, mm/gr, seemed to parallel the elongation whichhad occurred during pre-incubation, indicating that this value,contrary to To, represented at least partly the result of elongation. From these results we concluded that the growth rate to followis regulated by the minimum stress relaxation time, To, andpossibly by the relaxation rate, b, of the cell wall beforeextension, and these parameters may represent certain biochemicalmodifications of the cell wall components needed for cell extension. (Received August 12, 1974; )     

Membrane dynamics in mammalian embryogenesis: Implication in signal regulation

Eukaryotes have evolved an array of membrane compartments constituting secretory and endocytic pathways that allow the flow of materials. Both pathways perform important regulatory roles. The secretory pathway is essential for the production of extracellular, secreted signal molecules, but its function is not restricted to a mere route connecting intra‐ and extracellular compartments. Post‐translational modifications also play an integral function in the secretory pathway and are implicated in developmental regulation. The endocytic pathway serves as a platform for relaying signals from the extracellular stimuli to intracellular mediators, and then ultimately inducing signal termination. Here, we discuss recent studies showing that dysfunction in membrane dynamics causes patterning defects in embryogenesis and tissue morphogenesis in mammals. Birth Defects Research (Part C) 108:33–44, 2016. © 2016 Wiley Periodicals, Inc.     

Impact of Registered Dietitian Expertise in Health Guidance for Weight Loss

Background & Objectives

Expertise of registered dietitians (RDs) is important for health guidance but has been poorly evaluated. We evaluated the kind of RD expertise that would improve their skills.

Design, Setting, Participants, Measurements

This study was a post-hoc analysis of our randomized controlled trial, which compared the weight change between participants using the web-based self-disclosure health support and those using the email health support. Healthy men and women aged 35–64 years with a body mass index (BMI) of > = 24.5 kg/m² were recruited for this study. We evaluated the relationship of RD expertise indicators including the duration of working as an RD, the experience of health counseling, and membership in the Japan Dietetic Association (JDA) with the weight loss of study participants. The primary endpoint was the change in body weight. Comparison of changes in body weight by the RD expertise indicators was evaluated using analysis of covariance.

Results

A total of 175 participants were eligible for analyses. Changes in body weight were significantly greater when they were supported by the RDs in the routine counseling group than when supported by the RDs in the non-routine counseling group (-1.8 kg versus -0.4 kg, fully adjusted P = 0.0089). Duration of working as an RD and JDA membership did not significantly affect changes in body weight.

Conclusions

Among some indices of RD experience, the experience of providing routine experience of health counseling was associated with weight loss.