Typing method for N2-fixing bacteria based on PCR-F — application to the characterization of Frankia strains

DNA sequences of an intergenic spacer (IGS) and parts of genes in the nif cluster were amplified by the polymerase chain reaction (PCR) using two primers derived from nifD -and nifK -conserved sequences. The PCR products were cleaved by ten 4–base cutting restriction enzymes and the restriction patterns were used as fingerprints to type Frankia strains. The feasability of this PCR-RFLP method for typing Frankia strains was investigated on Frankia reference strains belonging mainly to the Elaeagnaceae infectivity group but also on new Frankia isolates and on other N₂-fixing microorganisms. By modulating the stringency of the amplifications, we showed the method allowed to target either Frankia strains or the whole N₂-fixing microbial community. DNA digestion patterns were used to estimate the sequence divergence between the Frankia nifD-K fragment. The estimated relationships deduced from these genotypic data correlated well with established Frankia taxonomic schemes.     

Increasing winter temperatures explain body size decrease in wintering bird populations of Northern Europe—But response patterns vary along the spatioclimatic gradient

Aim

Recent evidence has shown changes in body size and shape of individuals, which are suggested to be a result of global warming caused by climate change. Here, we explored the spatiotemporal changes in wing length and body mass of 24 wintering bird species in Northern Europe and how these relate to temperature anomaly.

Location

Finland and Sweden, Europe.

Time Period

50 years, 1970 to 2020.

Major Taxa Studied

Birds, 24 species.

Methods

We used site-specific, long-term winter ringing data containing wing length and body mass measurements from across Sweden and Finland for 24 bird species. We modelled wing length and body mass change over time, in relation to the spatioclimatic gradient and as response to temperature anomalies (of [i] the same winter as the ringing took place, [ii] the previous winter and [iii] the previous spring) by accounting for phylogenetic relatedness between species and their species-specific responses to each predictor of interest.

Results

We show that across all species, body size has decreased since the 1970s, with a negative relationship between wing length and temperature anomalies of previous winters, suggesting carry-over effects likely linked to body size-related survival or dispersal. Body mass was negatively related to the temperature anomaly of the same winter, indicating more immediate effects related to reduced fat reserves during mild winters.

Main Conclusions

Our results highlight a climate-driven decrease in body size across several species and its association with positive anomalies in winter temperature in the high latitudes. However, the responses are not spatially uniform and there is considerable species-specific variation, emphasizing the importance of conducting multispecies studies when investigating responses to climate change. The mechanisms of decreasing wing length and body mass seem to differ and underline the immediate and carry-over effects of temperature warming during the nonbreeding season.     

Environmental correlates of body size influence range size and extinction risk: A global study in rodents

Aim

Species-level traits, such as body and range sizes, are important correlates of extinction risk. However, both are often related and are driven by environmental factors. Here, we elucidated links between environmental factors, body size, range size and susceptibility to extinction, across the whole order of rodents.

Location

Global.

Time period

Current.

Major taxa studied

Rodents (order Rodentia).

Methods

We compiled an unprecedentedly large database of rodent morphology, phylogeny, range size, conservation status, global climate and normalized difference vegetation index (NDVI), comprising >86% of all described species. Using phylogenetic regressions, we initially explored the environmental factors driving body size. Next, we modelled the relationship between body size and range size. From this relationship, we computed and mapped (at the assemblage level) an index of relative range size, corresponding to the deviation from the expected range size of each species, given its body size. Finally, we tested whether relative range was correlated with the risk of extinction of the species derived from an assessment by the International Union for Conservation of Nature.

Results

We found that, contrary to the expectations of Bergmann's rule, the body size of rodents was mostly influenced by variation in NDVI (rather than latitude/temperature). Body size, in turn, imposed a constraint on species range size, as evidenced by a triangular relationship that was segmented at the lower bound. The relative species range size derived from this relationship highlighted four geographical regions where rodents with small relative range were concentrated globally. We demonstrated that lower relative range size was associated with increased risk of extinction.

Main conclusions

Species that, given their body size, are distributed across ranges that are smaller than expected have elevated extinction risk. Therefore, investigating the relationships between environmental drivers, body size and range size might help to detect species that could become threatened in the near future.     

Molecular Characterization of Human Rotavirus VP4 Genes by Polymerase Chain Reaction and Restriction Fragment Length Polymorphism Assay

A restriction fragment length polymorphism (RFLP) assay was developed to examine the genetic variability and similarity of the VP4 genes of human rotaviruses. The VP4 genes of 14 human rotavirus strains, including VP4 serotype P1A strains (Wa, P, VA70), serotype P1B strain (DS-1), serotype P2 strains (M37, 1076, McN, ST3) and serotype P3 strains (AU-1, AU228, K8, PA151, PCP5, MZ58), and those of 2 feline strains (FRV-1 and Cat2) were reverse-transcribed and amplified by the polymerase chain reaction (PCR). The amplified VP4 cDNAs were then digested with a panel of restriction endonucleases (HindIII, NruI, HaeIII, and EcoRI), resulting in the identification of at least one enzyme with which digestion produced an RFLP profile specific for a particular P serotype. Of interest was the presence of two distinct RFLP patterns within the serotype P3 VP4 genes: one corresponding to the VP4 gene carried by the members of the AU-1 genogroup and the other corresponding to the VP4 genes carried by naturally-occurring reassortants between members of the AU-1 and other genogroups.     

Length–biomass equations to allow rapid assessment of semi-aquatic bug biomass in tropical streams

Length–biomass equations are relatively easy and cost-effective for deriving insect biomass. However, the exact relationship can vary between taxa and geographical regions. Semi-aquatic bugs are abundant and are indicators of freshwater quality, but there are no studies investigating the effect of habitat disturbance on their biomass, although it is useful in assessing ecological processes. We identified the best-fit length–biomass models to predict the biomass of semi-aquatic bugs (Hemiptera, Gerromorpha) collected from streams in Sabah, Malaysia. We used 259 juvenile and adult semi-aquatic bugs to compare a range of plausible length–biomass functions, and to assess whether relationships differed across the following families and body forms: (1) Cylindrostethinae, Gerrinae, and Ptilomerinae, which are subfamilies within Gerridae consisting of small-to-large bugs that have long and slender bodies, (2) Halobatinae, a subfamily within Gerridae, consisting of small-to-medium bugs with wide heads and thoraxes as well as short abdomens, and (3) Veliidae, which are small bugs with stout bodies. Estimation used five fitting functions – linear regression, polynomial regression order 2, 3, and 4, and power regression – on the following groupings: three body forms combined; each body form with life stages (juvenile and adult) combined; and each body form with life stages separated. Power regressions were the best fit in predicting the biomass of semi-aquatic bugs across life stages and body forms, and the predictive power of models was higher when the biomass of different body forms was calculated separately (specifically for Halobatinae and Veliidae). Splitting by life stages did not always result in additional improvement. The equations from this study expand the scope of possible future ecological research on semi-aquatic bugs, particularly in Southeast Asia, by allowing more studies to consider biomass-related questions.     

IDENTIFICATION OF GEOGRAPHIC FORMS OF COMMON DOLPHIN (Delphinus delphis) FROM AERIAL PHOTOGRAMMETRY

Abstract: At least four morphologically distinct forms of common dolphins are found in the eastern Pacific, We compared length data for common dolphins photographed from the northern, central and southern regions as defined by Perrin et al. (1985) and found significant differences in average length for adult animals (>150 cm) and for "adult females" defined for our purposes as animals accompanied by calves. Analyses of calculated birth dates for calves demonstrated differences in timing of reproduction between the geographically adjacent forms. Length distributions from aerial photographs and samples collected from the purse seine fishery were strikingly similar. This work demonstrates a new, non-invasive method for obtaining unbiased life history and morphological data.     

Nuclear genomic composition of asymmetric fusion products between irradiated transgenic Solanum brevidens and S. tuberosum: limited elimination of donor chromosomes and polyploidization of the recipient genome

Summary The production of asymmetric somatic hybrid calli after fusion between gamma-irradiated protoplasts from transgenic Solanum brevidens and protoplasts from S. tuberosum are reported. Transgenic (kanamycin-resistant, GUS-positive) S. brevidens plants and hairy root clones were obtained after transformation with Agrobacterium tumefaciens LBA 1060 (pRi1855) (pBI121) and LBA 4404 (pRAL4404) (pBI121), and A. rhizogenes LBA 9402 (pRi1855) (pBI121), respectively. Leaf protoplasts isolated from the transgenic plants or root protoplasts from the hairy root clones were fused with S. tuberosum leaf protoplasts, and several calli were selected on kanamycin-containing medium. The relative nuclear DNA content of the hybrid calli was measured by flow cytometry (FCM), and the percentages of DNA of the S. brevidens and S. tuberosum genomes in the calli were determined by dot blot analysis using species-specific DNA probes. Chromosome-specific restriction fragment length polymorphism (RFLP) markers were used to investigate the elimination of specific S. brevidens chromosomes in the hybrids. The combined data on FCM, dot blot and RFLP analysis revealed that 18–62% of the S. brevidens DNA was eliminated in the hybrid calli and that the RFLP marker for chromosome 7 was absent in seven out of ten calli. The absence of RFLP markers for chromosomes 5 and 11 hardly ever occurred. In most of the hybrids the ploidy level of the S. tuberosum genome had increased considerably.     

Structure and evolution of the genomes ofsorghum bicolor andZea mays

Cloned maize genes and random maize genomic fragments were used to construct a genetic map of sorghum and to compare the structure of the maize and sorghum genomes. Most (266/280) of the maize DNA fragments hybridized to sorghum DNA and 145 of them detected polymorphisms. The segregation of 111 markers was analyzed in 55 F₂ progeny. A genetic map was generated with 96 loci arranged in 15 linkage groups spanning 709 map units. Comparative genetic mapping of sorghum and maize is complicated by the fact that many loci are duplicated, often making the identification of orthologous sequences ambiguous. Relative map positions of probes which detect only a single locus in both species indicated that multiple rearrangements have occurred since their divergence, but that many chromosomal segments have conserved synteny. Some sorghum linkage groups were found to be composed of sequences that detect loci on two different maize chromosomes. The two maize chromosomes to which these loci mapped were generally those which commonly share duplicated sequences. Evolutionary models and implications are discussed.     

A major photoperiod-sensitivity gene tagged with RFLP and isozyme markers in rice

Summary Photoperiod-sensitive rice (Oryza sativa L.) cultivars are widely grown in rainfed lowland areas with unfavorable water regimes. A molecular marker for the trait would be useful in genetic and physiological studies and in developing improved photoperiod-sensitive cultivars. Previous genetic studies identified a major gene for photoperiod sensitivity on chromosome 6. We have tested an isozyme marker and several RFLP probes mapping to chromosome 6 in an attempt to identify marker(s) tightly linked to photoperiod sensitivity in tropical rice cultivars. We report here that the isozyme gene Pgi-2 is linked (23.2±4.7 cM) to the photoperiod-sensitivity gene in the cultivar GEB-24. Although association of duration with Pgi-2 alleles can be used to detect segregation of the photoperiod sensitivity gene in crosses, it will probably not be useful as a marker in selection because of its loose linkage. In contrast, a gene for photoperiod sensitivity in the cultivar Puang Rai 2 was found to be closely linked to the rice genomic clone RG64. Among 15 F₃ lines homozygous for photoperiod insensitivity, no recombinants were detected with RG64. This clone is thus an excellent probe to follow segregation of the major photoperiod-sensitivity gene in rice crosses.     

Comparative genome analysis of mungbean (Vigna radiata L. Wilczek) and cowpea (V. unguiculata L. Walpers) using RFLP mapping data

Genome relationships between mungbean (Vigna tradiata) and cowpea (V. Unguiculata) based on the linkage arrangement of random genomic restriction fragment length polymorphism (RFLP) markers have been investigated. A common set of probes derived from cowpea, common bean (Phaseolus vulgaris), mungbean, and soybean (Glycine max) PstI genomic libraries were used to construct the genetic linkage maps. In both species, a single F₂ population from a cross between an improved cultivar and a putative wild progenitor species was used to follow the segregation of the RFLP markers. Approximately 90% of the probes hybridized to both mungbean and cowpea DNA, indicating a high degree of similarity in the nucleotide sequences among these species. A higher level of polymorphism was detected in the mungbean population (75.7%) than in the cowpea population (41.2%). Loci exhibiting duplications, null phenotypes, and distorted segregation ratios were detected in both populations. Random genomic DNA RFLP loci account for about 89% of the currently mapped markers with a few cDNA and RAPD markers added. The current mungbean map is comprised of 171 loci/loci clusters distributed in 14 linkage groups spanning a total of 1570cM. On the other hand, 97 markers covered 684 cM and defined 10 linkage groups in the current cowpea map. The mungbean and cowpea genomes were compared on the basis of the copy number and linkage arrangement of 53 markers mapped in common between the two species. Results indicate that nucleotide sequences are conserved, but variation in copy number were detected and several rearrangements in linkage orders appeared to have occurred since the divergence of the two species. Entire linkage groups were not conserved, but several large linkage blocks were maintained in both genomes.