A critique on the “Eight_Class System” of the classification of Angiosperms proposed by Wu et al.

Some critical comments are made on the “Eight-Classs System” of the classification of angiosperms recently proposed by Wu et al., which the aut hors claimed to be a “polyphyletic-polytopic” system. This system is established based on the hypothesis that there have existed eight principal lineages of angiosperms by the end of the Early Cretaceous. However, this hypothesis has not been supported by any neobotanical and paleobotanical evidence. There lationship among the eight lineages and their relationship with the common ances tor of angiosperms are not clearly clarified in the system. Having failed to follow the principle of common ancestry in the reconstruction of angiosperm phylogeny and having misinterpreted the concepts of monophyly and polyphyly, the “Eight-Class System” of the classification of angiosperms is considered to be an artificial one.     

A simplification of the protein assay method of Ramsay et al. for the quantification of Thiobacillus ferrooxidans in the presence of ferric precipitates

A variation on Ramsay's method for microbial protein determination has been developed in order to quantify Thiobacillus ferrooxidans attached to ferric precipitates or in aqueous suspensions containing such precipitates. Some modifications have been introduced to provide a method that is more sensitive, simple and rapid. A linear standard curve is presented to permit a direct correlation between the protein concentration (mg/l) and the cell concentration (10⁶ cells/ml). An application of this method has been demonstrated in the quantification of biomass immobilized on the surface of polyurethane foam particles in a packed bed reactor, several experiments having been conducted to establish the best conditions for the quantification studies. Received: 12 August 1999 / Received revision: 21 December 1999 / Accepted: 29 December 1999     

Early human dispersals into the Iberian Peninsula: a comment on Martínez et al.(2010) and Garcia et al. (2011)

Garcia et al. (2011) recently discussed early human dispersals into the Iberian Peninsula, describing several putative lithic artifacts (Martínez et al., 2010) recovered from layer 7 of the Vallpara díssection (Madurell-Malapeira et al., 2010) in Terrassa (Vallès-Penedès Basin, Catalonia, Spain). According to the authors' opinion, such evidence (1) fills a gap in the chronology of early human occupation in Iberia, (2) indicates that these populations had primary and early access to carcasses, and (3) confirms that early human populations were equipped with advanced cultural traits enabling them to survive in unfavourable climatic conditions. We argue below that the record of human activity at Vallparadís (Martínez et al., 2010;Garcia et al., 2011) is doubtful and even that if confirmed, a chronological gap would remain (contra Garcia et al., 2011). Additional remarks on assertions by these authors on the Vallparadís geology, taphonomy and paleonvironment are also provided.     

A study of the metabolism of l-αγ-diaminobutyric acid in a Xanthomonas species

1. l-αγ-Diaminobutyric acid is metabolized in Xanthomonas sp. to aspartic β-semialdehyde, aspartic acid and oxaloacetic acid. 2. Aspartic β-semialdehyde is formed from diaminobutyric acid by a pyruvate-dependent γ-transamination. 3. The transaminase has a pH optimum of 9 and exhibits a high degree of substrate specificity, as analogues of diaminobutyric acid and pyruvate are inert in the system. The transaminase is inhibited by carbonyl-binding agents such as hydroxylamine. 4. Aspartic acid is formed from aspartic β-semialdehyde by an NAD⁺-dependent dehydrogenation. 5. The dehydrogenase has a pH optimum of 8·5 and is a thiol enzyme. It is specific for aspartic β-semialdehyde but analogues of NAD⁺ such as 3-acetylpyridine–adenine dinucleotide and deamino-NAD are partly active in the system. 6. The significance of these reactions is discussed in relation to diaminobutyric acid metabolism in plants and mammalian systems.     

Reclassification of “Flavobacterium arborescens” (Frankland and Frankland) Bergey et al. in the genusMicrobacterium (Orla-Jensen) Collins et al., asMicrobacterium arborescens comb. nov., nom. rev.

Flavobacterium arborescens (Frankland and Frankland) Bergey et al. IFO 3750 (ATCC 4358) is a Gram-positive, coryneform bacterium and the only available reference strain of the species. The cell wall peptidoglycan of the organism possesses alanine, glycine, lysine, glutamic acid plus 3-hydroxyglutamic acid, and homoserine at a ratio of 1:3:1:1:1, and a possible peptidoglycan structure is the B1 type described by Schleifer and Kandler. Cell wall sugars are galactose, mannose, and 6-deoxy-l-talose, but not rhamnose. Major menaquinones are unsaturated MK-11 and MK-12. These findings and other taxonomic properties suggest that F. arborescens should be reclassified in the genusMicrobacterium (Orla-Jensen) Collins et al., asMicrobacterium arborescens comb. nov., nom. rev.     

Genome sequences and description of novel exopolysaccharides producing species Komagataeibacter pomaceti sp. nov. and reclassification of Komagataeibacter kombuchae (Dutta and Gachhui 2007) Yamada et al., 2013 as a later heterotypic synonym of Komagataeibacter hansenii (Gosselé et al. 1983) Yamada et al., 2013

Strains T5K1 and AV446 isolated from apple cider vinegars during a submerged vinegar production in two separate vinegar facilities showed 94% 16S rRNA gene similarity to its closest neighbors Komagataeibacter maltaceti LMG 1529^T and Gluconacetobacter entanii LTH 4560^T. Further phylogenetic and phenotypic characterizations indicated that the isolates belonged to a novel species of the Komagataeibacter genus. Comparison based on 16S–23S rRNA gene ITS sequences and concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, grouped both strains to a single phylogenetic cluster well separated from the other species of the Komagataeibacter genus. Average nucleotide identity of T5K1 and AV446 draft genome sequences compared to other Komagataeibacter type strains was below 94% and at the same time, in-silico DNA–DNA hybridization was below 70%. Both strains on the other hand showed approximately 98% (average nucleotide identity) and 87% (in silico DNA–DNA hybridization) similarity to each other. Strains T5K1 and AV446 can be differentiated from other Komagataeibacter type strains based on their ability to produce 2-keto-d-gluconic acid and at the same time inability to produce 5-keto-d-gluconic acid. Furthermore, strains of the new species do not grow on Asai medium supplemented with d-glucose or d-mannitol. The growth is also absent (T5K1) or weak (AV446) on Hoyer–Frateur medium supplemented with afore mentioned sugars. Both strains produce cellulose. In addition, draft genome analysis revealed that strains T5K1 and AV446 possess genes involved in the synthesis of acetan-like extracellular heteropolysaccharide. We propose the name Komagataeibacter pomaceti sp. nov. for the new species with LMG 30150^T [= CCM 8723^T = ZIM B1029^T] as the type strain. Data collected in this study and in a previous study also revealed that Komagataeibacter kombuchae is a later heterotypic synonym of Komagataeibacter hansenii.     

On the terms used to refer to ‘natural’ forests: a response to Veen et al.

The importance of harmonizing the group of terms used to indicate ‘natural’ forests is reported in several studies. In a recent paper the term virgin forest is proposed as a unifying concept for forests which are not influenced by man in their development. In response to that paper my aim is to clarify the terms virgin and old-growth. My response focuses on two points: the term virgin forest is generally used to indicate forests that have not been influenced by people even in the distant past, therefore something different from what described by the authors; the definition drawn up for the proposed term substantially overlaps with the definition of old-growth forest resulting from a long history of studies on this theme. I think that the overlap between the two analyzed terms can ultimately only increase the existing confusion on this group of forest terms.     

Assessing significance under the RMA ? moving forwards: a reply to Walker et al. (2008)

Walker et al. (2008) are critical of the methods used by ecologists and others with ?vested interests? to identify significant biodiversity values and provide for their protection under the Resource Management Act (1991) (RMA), particularly the use of the draft criteria proposed in Norton & Roper-Lindsay (2004). However, we believe that their criticism is flawed because of their failure to fully understand the context of the Norton?Roper-Lindsay criteria; unjustified presumptions they make about the roles of ecologists in assisting those applying for resource consents and administering the RMA; and a failure to take into account the current realities of native biodiversity conservation for those parts of New Zealand covered by the RMA. In this reply we address these issues and outline a way to move forwards in this debate.     

Speciation and chromosomal evolution of the Palearctic species of chironomids of the genus Sergentia Kieffer (Diptera, Chironomidae): Divergence of the Karyotypes of S. baueri Wülker et al., 1999, S. prima Proviz et al., 1997, S. electa Proviz et al., 1999 and their relationship with the endemic species from Baikal lake

The banding structures of chromosomes of three Palearctic species of chironomids of the genus Sergentia Kieffer, 1922 from the Irkutsk reservoir were comparatively analyzed: S. baueri Wülker et al., 1999 (2n = 8), S. prima Proviz et al., 1997 (2n = 8), and S. electa Proviz et al., 1999 (2n = 6). The S. baueri karyotype was taken as a standard in chromosome mapping. It was established that in contrast to S. baueri and S. prima the S. electa karyotype was formed due to a complex translocation: transfer of chromosome IV in the median part of chromosome III. The sequences of chromosome I bands were found to be completely homologous in all Palearctic species and in S. rara Proviz et al., 1999 (2n = 8) taken as the original species in the group of Baikalian endemics. In both groups, seven homozygous inversions were detected, of which the common one is the inversion in chromosome III. It was assumed on the basis of the results of the karyological analysis that among the Palearctic species S. baueri is most similar to the Baikalian endemics and S. electa is phylogenetically closer to S. prima. Specific features of the chromosome and morphological evolutions of the Sergentia genus species are considered.