Isozyme markers and volatiles in Tunisian Rosmarinus officinalis L. (Lamiaceae): A comparative analysis of population structure

Genetic and essential oil variations from 14 Tunisian natural populations of Rosmarinus officinalis L. were assessed using eight isozymes and 25 terpenoids. Isozymes were revealed by 13% gel electrophoresis. Volatiles were analysed by GC and GC–MS. Populations were collected from different regions belonging to sub-humid, upper semi-arid and upper arid bioclimates.     

Anatomy,trichome morphology and palynology of Salvia chrysophylla Stapf (Lamiaceae)

The anatomy, palynology, morphology and distribution of the trichomes on the aerial parts of Salvia chrysophylla Stapf, an endemic species in Turkey, were studied in order to understand the usefulness of these characteristics for systematic purposes. Some anatomical characters such as (1–)2–24-rowed pith rays in roots, dorsiventral leaves, obviously larger upper epidermal cells, and two to three large vascular bundles in the center and two to four small subsidiary bundles in the wings of petiole provide information of taxonomical significance. Three main types of trichomes were observed on the stem, inflorescence axis, leaf and calyx surfaces of S. chrysophylla. They are peltate, capitate glandular and non-glandular. Capitate glandular and non-glandular trichomes were further subdivided into several kinds. Glandular trichomes are present in abundance on the inflorescence axis and calyx, but non-glandular ones were mainly situated on the leaf and stem. Scanning Electron Microscopy (SEM) studies on the pollen grains have revealed that they are oblate-spheroidal and their exine ornamentation is bireticulate-perforate.     

A novel method based on high resolution melting (HRM) analysis for MIRU-VNTR genotyping of Mycobacterium tuberculosis

The mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) method is one of the most important methods that have been used in recent years for genotyping Mycobacterium tuberculosis. Agarose gel electrophoresis and capillary electrophoresis have been used to determine the size of amplicons, however, both of these methods have shortcomings. Here, we develop and evaluate a novel method for MIRU-VNTR typing based on high resolution melting (HRM) analysis. The MIRU40 locus was selected to evaluate different real-time PCR machines and the accuracy of our method; the Roche LightCycler 480 provided greatest consistency between the T_m value and repeat number and was used in subsequent evaluations. Our method gives greater accuracy in comparison with conventional agarose gel electrophoresis (98.9% vs. 90.9%, p = 0.017), and, with the help of fitting formulae, can be used to obtain the number of MIRU tandem repeats from the T_m value. To validate our method we analyzed 12 classical MIRU loci to genotype 88 clinical isolates. The number of MIRU tandem repeats was determined accurately, quickly and conveniently.     

Experimental study of enriched frozen diet on digestive enzymes and growth of juvenile cuttlefish Sepia officinalis L. (Mollusca Cephalopoda)

Hatchlings cuttlefish were reared in the laboratory from hatching until 30 days old, fed with live shrimp, frozen shrimp or fish oil-enriched frozen shrimp. Survival of cuttlefish fed with oil-enriched frozen shrimp was better than in animals receiving live shrimp. However, there was no difference with cuttlefish fed with frozen shrimp, even if survival of those receiving oil-enriched frozen shrimp was always higher all along the experiment. Lower survival in animals fed with live shrimp represented the problem of using such food and confirms the necessity to elaborate an artificial food. Utilization of artemia was detrimental to growth and induced low values of instantaneous growth rate (IGR) and conversion rate even after feeding cuttlefish with shrimp. Nevertheless, growth parameters evolutions generally corresponded to those observed by other researchers. The profile noticed at the end of the experiment is typically observed when cuttlefish acquire their adult digestive system. Main differences were observed between groups fed with live shrimp or oil-enriched frozen shrimp. Enrichment did not induce same growth as in cuttlefish receiving live prey. However, at 20 and 25 days after hatching (DAH), in cuttlefish fed with oil-enriched frozen shrimp, ration was lower for the same growth than in other groups.These data showed capacity of juvenile cuttlefish to adjust their digestive enzyme activities according to the diet and the stage of development. Indeed, chymotrypsin was strongly influenced by enrichment, while other enzymes showed difference between live and frozen preys. Trypsin exhibited regulation by diet after 20 DAH. Freezing seemed to delay development as acid phosphatases, characteristic of first stages of cuttlefish, had lower activity in cuttlefish fed with live shrimp at 10 DAH. Moreover, influence of the stage of development was strong as activities between 20 and 30 DAH were different in all groups. This was in relation with evolution of the digestive system. These data illustrated the difficulty to elaborate optimal diet as digestive system evolves.     

Structural investigation of the glandular trichomes of endemic Salvia smyrnea L.

The morphology, anatomy and distribution of glandular trichomes on the aerial organs of Salvia smyrnea L. endemic to Turkey have been investigated with light microscopy (LM) and scanning electron microscopy (SEM). This species is evaluated in endangered (EN) category. Two morphologically distinct types of glandular trichomes were determined. Various types of capitate glandular trichomes consist of a 1–4 celled base, a 1–8 stalk celled or no stalk and a uni- or bicellular head.     

Pollen morphology of the genus Salvia L. (Lamiaceae) in Turkey

Pollen grains of 30 taxa of the genus Salvia, belonging to sections Salvia, Horminum, Drymosphace, Plethiosphace and Hemisphace from Turkey were examined by light (LM) and scanning electron microscopy (SEM). Detailed pollen morphological characteristics are provided for these taxa. Among the studied taxa, S. verticillata subsp. verticillata from sect. Hemisphace has the smallest pollen grains, and S. pachystachys from sect. Salvia possesses the largest ones. The basic shape of the pollen grains in most taxa is suboblate, oblate-spheroidal or prolate-spheroidal. However subprolate pollen grains are recorded for S. macrochlamys from sect. Salvia. The grains are hexacolpate in all taxa, but in S. recognita from sect. Salvia also octacolpate pollen was found. Three distinct exine sculpturing types exist, reticulate-perforate (the common type), reticulate-granulate and bireticulate. The reticulate-perforate and bireticulate sculpturing patterns can be divided into subtypes based on the number of perforations and the number of secondary lumina in each primary lumen. Pollen morphological characteristics of the taxa studied are compared and discussed on the basis of taxonomical concepts. In some cases, these characters are useful in distinguishing the sections. For instance, the presence of 1-2 large central secondary lumina per primary lumen is a significant character of sect. Horminum separating it from the other sections. As well, the presence of holes on colpus membrane ornamentation can be used as a diagnostic taxonomic character for sectional division between sect. Hemisphace and others. S. ballsiana from sect. Salvia is clearly distinct from the other taxa examined by its unique pollen morphology. Further, for several macromorphologically similar taxa pollen structures provide additional evidence to delimite them from each other.     

Population genetic differentiation of Schisandra chinensis and Schisandra sphenanthera as revealed by ISSR analysis

Schisandra chinensis (Turcz.) Baill. and Schisandra sphenanthera Rehd. et Wils. are well-known Chinese medicinal plants. The population genetic variation of the two species was studied using inter simple sequence repeat (ISSR) molecular markers. High levels of genetic diversity are revealed in both S. chinensis (P = 88.36%, h = 0.2894, I = 0.4396) and S. sphenanthera (P = 84.09%, H = 0.2782, I = 0.4280). However, the population genetic differentiation is significantly different between the two species. The S. sphenanthera harbors as high as 27% of the genetic variation among populations but 73% within populations, whereas in S. chinensis 17% of the genetic variation occurs among populations and 83% within populations. Both significant (P < 0.05) heterozygosity excess and shifted mode of allele frequency distribution are detected in four out of six populations of S. chinensis and one out of five populations of S. sphenanthera, suggesting the occurrence of recent population bottlenecks in the two species. The different patterns of genetic variation in S. chinensis and S. sphenanthera are discussed in relation to their differences in pollination mechanism, geographic distribution and historical events, and the level of gene flow and genetic drift.     

Factors influencing seed germination of medicinal plant Salvia aegyptiaca L. (Lamiaceae)

Salvia aegyptiaca is a xerophytic perennial herb belongs to the Lamiaceae family commonly used for medicinal purposes. Laboratory experiments were carried out to assess the effects of temperature and salinity on seed germination and recovery responses after transferring to distilled water. Temperatures between 10 and 40 °C seem to be favourable for the germination of this species. Germination was inhibited by either an increase or decrease in temperature from the optimum (30 °C). The highest germination percentages were obtained at 0 mM NaCl; however, the increase of solution osmolalities progressively inhibited seed germination. The germination rate decreased with an increase in salinity for most of tested temperatures, but comparatively higher rates were obtained at 30 °C. Salt stress decreased both the percentage and the rate of germination. An interaction between salinity and temperature yielded no germination at 300 mM NaCl. By experimental transfer to distilled water, S. aegyptiaca seeds that were exposed to moderately saline conditions recovered and keep their ability to germinate mostly at low temperatures. At 300 mM NaCl, germination recovery decreased with increasing temperature and it was completely inhibited at 40 °C.     

Determination of phenolic antioxidant compounds produced by calli and cell suspensions of sage (Salvia officinalis L.)

Sage (Salvia officinalis L.) calli were established by culturing internodal segments, excised from aseptic seedlings, on MS basal medium gellied with agar and supplemented with 0.05 mg/L dichlorophenoxyacetic acid (2,4-D) in presence of benzyladenine (BA) or zeatin (ZEA) or kinetin (KIN), at 1.5 mg/L. Suspended cells were established by transferring one callus to 50 mL of liquid MS basal medium devoid of agar and containing the same type of hormonal supplementation used in respective calli growth. The highest growth of calli and suspensions occurred with 1.5 mg/L ZEA. However, with this cytokinin supplementation, as well as with 1.5 mg/L KIN, both in presence of 0.05 mg/L 2,4-D, suspensions differentiated small root shaped structures. Well shaped, majority single cell suspensions were formed under the effect of 0.05 mg/L 2,4-D and 0.5 mg/L KIN. Calli grown with 0.05 mg/L 2,4-D and 1.5 mg/L BA and suspended cells grown with 0.05 mg/L 2,4-D and ZEA or KIN at 1.5 mg/L, or KIN at 0.5 mg/L, were searched for phenolics production. Twelve phenolic compounds were identified in calli: gallic acid, 3-O-caffeoylquinic acid, 5-O-caffeoylquinic acid, caffeic acid, rosmarinic acid, hesperetin, epirosmanol, hispidulin, genkwanin, carnosol, carnosic acid, and methyl carnosate. With the exception for genkwanin and epirosmanol all of these phenolic compounds were also produced by the sage suspension cultures grown in the presence of 1.5 or 0.5 mg/L KIN. Genkwanin was the only phenolic absent in the suspensions grown with 1.5 ZEA. Suspended cells, grown with 0.5 mg/L KIN, and calli cultures showed the highest specific accumulation of the total phenolics, with rosmarinic acid representing 94-97 percnt;.     

High resolution melting PCR to differentiate Mycobacterium avium subsp. paratuberculosis"cattle type" and "sheep type"

In this study, we describe a novel HRM-PCR assay that clearly differentiates the two main types of Mycobacterium avium subsp. paratuberculosis (cattle and sheep) based on the polymorphic variation of a previously described tandem repeat. This modern genotyping technique has several advantages over alternative methods, including cost, ease of use and rapidity.     

Identification of fibrillin-1 gene mutations in Marfan syndrome by high-resolution melting analysis

Marfan syndrome has been associated with approximately 562 mutations in the fibrillin-1 (FBN1) gene. Mutation scanning of the FBN1 gene with DNA direct sequencing is time-consuming and expensive because of its large size. This study analyzed the diagnostic value of high-resolution melting analysis as an alternative method for scanning of the FBN1 gene. A total of 75 polymerase chain reaction (PCR) amplicons (179-301 bp, average 256 bp) that covered the complete coding regions and splicing sites were evaluated on the 96-well LightCycler system. Melting curves were analyzed as fluorescence derivative plots (−dF/dT vs. temperature). To determine the sensitivity of this method, a total of 82 samples from patients with Marfan syndrome and 50 unaffected individuals were analyzed. All mutations reported in this study had been confirmed previously by direct sequencing analysis. Melting analysis identified 48 heterozygous variants. The variant c.3093 G>T (exon 25) was incorrectly identified by melting curve analysis. The sensitivity of the technique in this sample was 98.78% (81/82). This study demonstrated that high-resolution melting analysis is a reliable gene scanning method with greater speed than DNA sequencing. Our results support the use of this technology as an alternative method for the diagnosis of Marfan syndrome as well as its suitability for high-throughput mutation scanning of other large genes.     

Chloroplast DNA analysis in Tunisian fig cultivars (Ficus carica L.): Sequence variations of the trnL-trnF intergenic spacer

We investigated the nucleotide variation of a non-coding, chloroplast DNA (cpDNA) region to infer relationships among Tunisian fig cultivars. In this study, we examine the level of genetic diversity and its distribution using sequences of the trnL and trnF genes intergenic spacer. The non-coding region displays 28 substitution sites. Insertions and deletions involving 6 sites were found. By using the Kimura-2 method, nucleotide sequences have been aligned using the MEGA program to calculate pairwise divergence of trnL-trnF spacer sequences between cultivars. The size of this non-coding region varied from 430 to 464 bases. The relatively high A + T values (63.7–64.4%) of trnL-trnF intergenic spacer in Ficus carica may explain the high proportion of the identified transversions (t_i/t_v = 0.9). These results suggest the occurrence of nucleotide diversity with a large variation level of chloroplast non-coding region. The analysed data illustrate a considerable level of variability in the genetic pool of the local germplasm. In fact, relationships inferred from the cpDNA analysis suggest several clades, which do not show geographical correspondence. Fourteen haplotypes were detected among 20 individuals examined, yielding a haplotype diversity of 0.983 and a high level of nucleotide diversity (0.0100). The observed variation pattern of plastid DNA provides evidence that the fig germplasm has been undergoing rapid expansion. Neutrality tests rejected the neutrality assumption in the total sample. The cytoplasm variability indicates a narrow genetic base in the cultivated common fig. Despite the high level value of the apparent diversity, we may conclude that fig chloroplast genome provides a new conceptual and practical opportunity to evaluate genetic diversity and to identify local cultivars, making it a valuable source to include into potential breeding programs.     

Optimization of melting analysis with TaqMan probes for detection of KRAS,NRAS, and BRAF mutations

The TaqMan probes that have been long and effectively used in real-time polymerase chain reaction (PCR) may also be used in DNA melting analysis. We studied some factors affecting efficiency of the approach such as (i) number of asymmetric PCR cycles preceding DNA melting analysis, (ii) choice of fluorophores for the multiplex DNA melting analysis, and (iii) choice of sense or antisense TaqMan probes for optimal resolution of wild-type and mutant alleles. We also determined ΔT_m (i.e., the temperature shift of a heteroduplex relative to the corresponding homoduplex) as a means of preliminary identification of mutation type. In experiments with serial dilution of mutant KRAS DNA with wild-type DNA, the limit of detection of mutant alleles was 1.5–3.0%. Using DNA from both tumor and formalin-fixed paraffin-embedded tissues, we demonstrated a high efficiency of TaqMan probes in mono- and multiplex mutation scanning of KRAS, NRAS (codons 12, 13, and 61), and BRAF (codon 600) genes. This cost-effective method, which can be applied to practically any mutation hot spot in the human genome, combines simplicity, ease of execution, and high sensitivity—all of the qualities required for clinical genotyping.     

Observation of eight ancient olive trees (Olea europaea L.) growing in the Garden of Gethsemane

For thousands of years, olive trees (Olea europaea L.) have been a significant presence and a symbol in the Garden of Gethsemane, a place located at the foot of the Mount of Olives, Jerusalem, remembered for the agony of Jesus Christ before his arrest. This investigation comprises the first morphological and genetic characterization of eight olive trees in the Garden of Gethsemane. Pomological traits, morphometric, and ultrastructural observations as well as SSR (Simple Sequence Repeat) analysis were performed to identify the olive trees. Statistical analyses were conducted to evaluate their morphological variability. The study revealed a low morphological variability and minimal dissimilarity among the olive trees. According to molecular analysis, these trees showed the same allelic profile at all microsatellite loci analyzed. Combining the results of the different analyses carried out in the frame of the present work, we could conclude that the eight olive trees of the Gethsemane Garden have been propagated from a single genotype.     

Development of a bioassay from isolated digestive gland cells of the cuttlefish Sepia officinalis L. (Mollusca Cephalopoda): effect of Cu, Zn and Ag on enzyme activities and cell viability

The purpose of this study was to establish a bioassay from isolated digestive gland cells of the cuttlefish Sepia officinalis in order to observe the effect of heavy metals on digestive enzyme activities. Digestive cells were isolated using a pronase enzyme that was removed by several washings of the cell suspension. Cell viability was tested by the MTT assay (3-4,5-dimethylthiazol-2-yl-2,5-diphenyl tetrazolium) and microscopic analysis. The results showed that isolated digestive cells could be maintained 24 h with preservation of whole digestive functionality, measured in terms of MTT test. In fact, the viability was maintained at a high level during 24 h and the intra- and extracellular digestive enzyme activities became stabilised rapidly. Furthermore, suspension cells responded to calcium ionophore and 8-Bromo-cAMP by an unspecific secretion of extracellular digestive enzyme, trypsin, which demonstrated that isolated digestive cells were functional. Using the bioassay, ecotoxicological studies showed that heavy metals could have effects on digestive enzyme activities after 24 h of an incubation time of the metal with the cells. In fact, zinc and silver affected trypsin and/or cathepsins specific activity of the cells. On the contrary, copper had no effect on digestive enzyme activities. Zinc, which is a trace element in all living animals, generated two different responses of cathepsins and cell viability. At a low concentration (0.02 μM), it increased viability and cathepsins specific activity, whereas at a high concentration (0.02 mM), zinc inhibited the cathepsins specific activity with an inhibition of cathepsins. For silver, whatever the tested concentration (0.02 mM or 0.02 μM), it has no impact on digestive gland isolated cell viability. Nevertheless, heavy metal induced high disturbance of enzymatic systems.     

Fate of resting cysts of Alexandrium spp. ingested by Perinereis nuntia (Polychaeta) and Theola fragilis (Mollusca)

The ingestion of resting cysts of Alexandrium spp. by Perinereis nuntia (Polychaeta) and Theola fragilis (Mollusca) was experimentally examined in the laboratory. P. nuntia and T. fragilis were cultured in bottom sediment containing a high density of Alexandrium cysts under dark conditions. Moreover, to evaluate the degree and consequence of being ingested, the density of cysts in the control sediment (no macrobenthic organisms) and the germination capability of the cysts in the faecal pellets of the two species of macrobenthos were examined.Cysts in the culture sediment were found to be ingested by both P. nuntia and T. fragilis. No difference in the density of cysts between the sediments cultured with and without P. nuntia was observed. However, the density of cysts in the sediments with T. fragilis decreased by 24% compared to the density in the control sediment. It is possible that most of the cysts ingested were digested by T. fragilis. The rate of Alexandrium cyst digestion by this species is estimated 594 cysts/individual/day. It is estimated that 91% of the cysts ingested by T. fragilis were partially or totally digested and only 9% were excreted in a viable state during the experiment. Thus, T. fragilis has a stronger affect on the abundance of Alexandrium cysts compared with P. nuntia.No significant difference was observed between the germination success of the cysts from faecal pellets of P. nuntia and T. fragilis compared to the cysts in the control sediment. If, however, the necessary light for the cysts to germinate is cut off by being enclosed within the faecal pellet, the germination rate of cysts from the faecal pellets may be suppressed.