Plant Fragments Research Articles

A protocol for obtaining DNA barcodes from plant and insect fragments isolated from forensic-type soils.

Soil is often collected from a suspect's tire, vehicle, or shoes during a criminal investigation and subsequently submitted to a forensic laboratory for analysis. Plant and insect material recovered in such samples is rarely analyzed, as morphological identification is difficult. In this study, DNA barcoding was used for taxonomic identifications by targeting the gene regions known to permit discrimination in plants [maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL)] and insects [cytochrome oxidase subunit I (COI)]. A DNA barcode protocol suitable for processing forensic-type biological fragments was developed and its utility broadly tested with forensic-type fragments (e.g., seeds, leaves, bark, head, legs; n, 213) isolated from soils collected within Virginia, USA (n, 11). Difficulties with PCR inhibitors in plant extracts and obtaining clean Sanger sequence data from insect amplicons were encountered during protocol development; however, the final protocol produced sequences specific to the expected locus and taxa. The overall quantity and quality of DNA extracted from the 213 forensic-type biological fragments was low (< 15ng/μL). For plant fragments, only the rbcL sequence data was deemed reliable; thus, taxonomic identifications were limited to the family level. The majority of insect sequences matched COI in both GenBank and Barcode of Life DataSystems; however, they were identified as an undescribed environmental contaminant. Although limited taxonomic information was gleaned from the forensic-type fragments processed in this study, the new protocol shows promise for obtaining reliable and specific identifications through DNA barcoding, which could ultimately enhance the information gleaned from soil examinations.

Modified cleaning method for biomineralized components

Abstract. The extraction and concentration of biomineralized components from sediment or living materials is time consuming and laborious and often involves steps that remove either the calcareous or siliceous part, in addition to organic matter. However, a relatively quick and easy method using a commercial cleaning fluid for kitchen drains, sometimes combined with a kerosene soaking step, can produce remarkable results. In this study, the method is applied to sediments and living materials bearing calcareous (e.g., coccoliths, foraminiferal tests, holothurian ossicles, ichthyoliths, and fish otoliths) and siliceous (e.g., diatom valves, silicoflagellate skeletons, and sponge spicules) components. The method preserves both components in the same sample, without etching or partial dissolution, but is not applicable to unmineralized components such as dinoflagellate thecae, tintinnid loricae, pollen, or plant fragments.

Food and Feeding Habits of Gaur (Bos gaurus) in Highlands of Central India: A Case Study at Pench Tiger Reserve, Madhya Pradesh (India).

Indian gaur (Bos gaurus) is one of nine species of wild oxen found in the world. They are largely confined to evergreen, semi-evergreen, and moist deciduous forests, but also occur in dry deciduous forest areas at the periphery of their range. According to the IUCN Red List ( 2017 ), the estimated population of gaur in India is between 15,000 and 35,000 individuals, and probably due to this, despite the gaur's vast range of distribution, they are listed as a vulnerable species by IUCN and listed as schedule-I of the Indian Wildlife Protection Act ( 1972 ) as well as in appendix-I in CITES ( 2003 ). Gaur is not a well studied species, and baseline data are thus needed to support conservation efforts. We studied the feeding habits of gaur in Pench Tiger Reserve. Pench Tiger Reserve is the 19th tiger reserve in India, situated in the Seoni and Chhindwara districts of MP, India (21°41'35″N 79°14'54″E). Diet composition of gaur was studied by micro-histological examination of 32 dung piles collected from different sampling plots in different seasons. For this purpose, 169 sampling plots were established at an interval of 200 m. To locate gaur faecal matter, a circular plot of 10 m radius was laid within each sampling plot. Eighty-eight permanent reference slides of available plants were prepared and used for plant fragment identification from the dung piles. A total of 29 plant species were identified from dung piles of gaur. On average, 44.51% of grass-fragments were detected in the diet of gaur, suggesting that gaurs are primarily grazers in the Pench Tiger Reserve.

Enzymatic chemical transformations of aldehydes, ketones, esters and alcohols using plant fragments as the only biocatalyst: Ximenia americana grains

The present study demonstrated the ability of Ximenia american as a biocatalyst in reduction, hydrolysis and esterification reactions. The reduction reactions of aldehydes and ketones, ester hydrolysis and esterification of alcohols were carried out with interesting results. Reduction of ketones afforded yields of 6–60% with ee in the range of 35–>99% and that of aldehydes in yields of 51–99%. On the other hand, ester hydrolysis afforded yields of 58–98% with ee in the range 34–87%, while esterification of alcohols in 18–99% yields. Experimental conditions for all reactions have been defined using standard substrates as indicated in results and discussion. Some of the products are the potential building blocks for the synthesis of molecules which are of pharmaceutical and agrochemical importance.

Microbial-caddisfly bioherm association from the Lower Cretaceous Shinekhudag Formation, Mongolia: Earliest record of plant armoring in fossil caddisfly cases.

Caddisfly larvae construct underwater protective cases using surrounding materials, thus providing information on environmental conditions in both modern and ancient systems. Microbial bioherms associated with caddisfly cases are found in the Berriassian-Hauterivian (~140–130 Ma) Shinekhudag Formation of Mongolia, and yield new insights into aspects of lacustrine paleoecosystems and paleoenvironments. This formation contains the earliest record of plant-armored caddisfly cases and a rare occurrence of microbial-caddisfly association from the Mesozoic. The bioherms are investigated within the context of stratigraphic correlations, depositional environment interpretations, and basin-evolution models of the sedimentary fill. The bioherms form 0.5–2.0 m diameter mound-shaped bodies and are concentrated within a single, oil shale-bound stratigraphic interval. Each bioherm is composed of up to 40% caddisfly cases along with stromatolites of millimeter-scale, micritic laminations. Petrographic analyses reveal these bioherms are composed of non-systematic associations of columnar and oncoidal microbialites, constructed around colonies of caddisfly cases. The cases are straight to curved, slightly tapered, and tube-shaped, with a progressively increasing length and width trend (7–21 mm by 1.5–2.5 mm). Despite these variations, the case architectures reveal similar construction materials; the particles used for cases are dominated by plant fragments, ostracod valves, carbonate rocks, and rare mica and feldspar grains. Allochems within the bioherms include ooids, ostracods, plant fragments, rare gastropods, feldspar grains bound in micritic matrices, and are consolidated by carbonate dominated cements. The combination of microbial-caddisfly association, plant fragment case particles, and ooids/oncoids are indicative of a shallow, littoral lake setting. Stratigraphic juxtaposition of nearshore bioherms and the bounding distal oil-shale facies suggests that the bioherms developed in an underfilled lake basin, resulting from an abrupt and short-lived lake desiccation event. Lake chemistry is believed to have been relatively alkaline, saline to hypersaline, and rich in Ca, Mg, and HCO3 ions. Through analyzing bioherm characteristics, caddisfly case architecture, carbonate microfacies, and stratigraphic variability, we infer larger-scale processes that controlled basin development during their formation.

Gymnocoronis spilanthoides

Gymnocoronis spilanthoides

Activity of the Funai Fault and Radiocarbon Age Offsets of Shell and Plant Pairs from the Latest Pleistocene to Holocene Sediments Beneath the Oita Plain, Western Japan

AbstractBeppu Bay is located on east-central Kyushu, southwest Japan, and is characterized by hydrothermal activity, tectonic deformation, and recent volcanism under the influence of convergence of the Philippine Sea plate. This area, occupying the western portion of an arc-bisecting dextral fault system, is a tectonic depression that has existed since ca. 5 Ma. Sedimentary facies, mollusk assemblages, and radiocarbon (14C) ages of 25 terrestrial plant fragments and 16 marine carbonate shells from a 70-m drill core were determined to estimate the activity of the Funai Fault, which consists of normal faults along the southern margin of the tectonic basin. Based on the analysis, six sedimentary facies, namely braided river channel, estuary, prodelta, delta front, delta plain, and artificial soil, were identified. The vertical slip rate was calculated as 2.6–2.7 mm/yr based on displacements of the braided river channel sediments of the last glacial period and the base of Kikai-Akayoya tephra in the Holocene highstand sediments of this area. Reservoir ages during 6180–10,410 cal BP were determined from marine shell and terrestrial plant pairs from the sediments of the estuary, prodelta and delta front facies, and were correlated with values from a northern coast of Kyushu and the Korean Peninsula.

Seasonal variability of carbon in humic-like matter of ambient size-segregated water soluble organic aerosols from urban background environment

Long-term measurements of carbon in HUmic-LIke Substances (HULIS-C) of ambient size-segregated water soluble organic aerosols were performed using a ten-stage low-pressure Berner impactor from December 2014 to November 2015 at an urban background environment in Ljubljana, Slovenia. The mass size distribution patterns of measured species (PM - particulate matter, WSOC - water-soluble organic carbon and HULIS-C) for all seasons were generally tri-modal (primarily accumulation mode) but with significant seasonal variability. HULIS-C was found to have similar distributions as WSOC, with nearly the same mass median aerodynamic diameters (MMADs), except for winter when the HULIS-C size distribution was bimodal. In autumn and winter, the dominant accumulation mode with MMAD at ca. 0.65 μm contributed 83 and 97% to the total HULIS-C concentration, respectively. HULIS-C accounted for a large fraction of WSOC, averaging more than 50% in autumn and 40% in winter. Alternatively, during warmer periods the contributions of ultrafine (27% in summer) and coarse mode (27% in spring) were also substantial. Based on mass size distribution characteristics, HULIS-C was found to be of various sources. In colder seasons, wood burning was confirmed as the most important HULIS source; secondary formation in atmospheric liquid water also contributed significantly, as revealed by the MMADs of the accumulation mode shifting to larger sizes. The distinct difference between the spring and summer ratios of HULIS-C/WSOC in fine particles (ca. 50% in spring, but only 10% in summer) indicated different sources and chemical composition of WSOC in summer (e.g., SOA formation from biogenic volatile organic compounds (BVOCs) via photochemistry). The enlarged amount of HULIS-C in the ultrafine mode in summer suggests that the important contribution was most likely from new particle formation during higher emissions of BVOC due to the vicinity of a mixed deciduous forest; the higher contribution of HULIS-C in the coarse mode demonstrated that beside soil erosion other sources, such as pollen and plant fragments, could also be responsible.

Tephra identification and radiocarbon chronology of sediment from Paitan Lake at the northern part of Luzon Central Plain, Philippines

In order to construct the tephrostratigraphy of the northern region of the Philippines, two sediment cores were obtained from Paitan Lake. Paitan Lake is located in the northern part of Luzon Central Plain, 88 km northeast of Pinatubo Volcano. It's a crater lake with a surface area of 0.8 km2. Its drainage basin has an area of 38.5 km2 and has an outflow-river with a width of only a few meters. These cores consisted of two units: (1) an upper alternating bed of mud and peaty layers, from depths 0–6 m; and (2) a lower dark gray to gray mud bed, obtained from depths 6–28 m. Eight tephras were recognized, on the split surface of the cores. Radiocarbon ages of seven plant fragments, from 1.50 to 13.41 m depths, and twelve organic sediments, from 4.72 to 28.00 m depths were measured by the AMS facilities of KIGAM, Nagoya University and Institute of Accelerator Analysis Ltd. These results were 1.6–24 cal kBP. These ages of tephras were correlated to the eruption periods of Pinatubo and Natib Volcano.

Biodiversity of pollen in indoor air samples as revealed by DNA metabarcoding

We conducted DNA metabarcoding (based on the nuclear ITS2 region) to characterize indoor pollen samples (possibly accompanied by other plant fragments) and to discover whether there are seasonal changes in their taxonomic diversity. It was shown that DNA metabarcoding has potential to allow a good discovery of taxonomic diversity. The number of spermatophyte families and genera varied greatly among sampling sites (pooled results per building) and times, between 9–40 and 10–66, respectively. Comparable Shannon's diversity indices equaled 0.33–2.76 and 0.94–3.16. The total number of spermatophyte genera found during the study was 187, of which 43.9, 39.6, 7.5 and 9.1% represented wild, garden/crop and indoor house plants, and non‐domestic fruit or other plant material, respectively. Comparable proportions of individual sequences equaled 77.4, 18.8, 2.7 and 1.1%, respectively. When comparing plant diversities and taxonomic composition among buildings or between seasons, no obvious pattern was detected, except for the second summer, when pollen coming from outdoors was highly dominant and the proportions of likely allergens, birch, grass, alder and mugwort pollen, were very high. The average pairwise values of SørensenChao indices that were used to compare similarities for taxon composition between samples among the samples from the two university buildings, two nurseries and farmhouse equaled 0.514, 0.109, 0.564, 0.865 and 0.867, respectively, while the mean similarity index for all samples was 0.524. Cleaning frequency may strongly contribute to the observed diversity. The discovery of considerable diversities, including pollen coming from outside, in both winter and summer shows that substantial amounts of pollen produced in summer enter buildings and stay there throughout the year.

Study of Sedative Tea Phytocomplex within the Framework of Studies Aimed at Creation of a Rectal Dosage Form with Antihistaminic Effect

We designed a new complex drug with antiallergic effect containing, in addition to the main component loratadine, a phytocomplex for an extra therapeutic effect. A collection of plants with sedative activity is chosen and the optimal agent for extraction of bioactive compounds (40% ethanol) and optimal degree of plant fragmentation are determined. Chemical composition of the sedative tea is evaluated by reverse phase HPLC. The marker components of the species are detected: xanthohumol and isoxanthohumol - Humulus lupulus cone components, Mentha piperita rosmarinic acid, and scutellareine, Menyanthes trifolia element - quercetin-3-rutinoside, and caffeic acid. Standardization of the species by the absolute graduation method in conversion to quercetin-3-rutinoside is suggested.

Petrography and Environmental Interpretation of Tufa Mounds and Carbonate Beds In the Jurassic Navajo Sandstone of Southeastern Utah, U.S.A.

Abstract: Carbonate deposits in the Jurassic Navajo Sandstone of Utah reflect deposition in interdune lakes and springs. Interdune-lake deposits consist of flat-lying carbonate units. Springs formed tufa mounds that are interpreted as subaerial, ambient-temperature, artesian-spring deposits. In the first systematic study of the petrography of the carbonate deposits in the Navajo Sandstone, eleven facies were identified in several flat-lying carbonate deposits and two tufa mounds. Fenestral mudstone and peloidal facies dominate the lacustrine deposits, whereas thrombolitic mudstone characterizes the mounds. The biota consists of ostracodes, charophytes, fish, mollusks, a possible freshwater sponge, trace fossils, and fragments of vascular plants. Features resulting from penecontemporaneous weathering provide evidence of episodic exposure of the lacustrine carbonate beds during deposition and formation of the tufa mounds under subaerial conditions. Although carbonate deposits are not rare in eolian systems, few have been studied in detail; comparisons between these and the Navajo Sandstone carbonate deposits reveal some characteristics that may be unique to the latter.

Expression of potato virus S gRNA fragments in transgenic potato plants triggers RNA-interference against related and unrelated viruses

This chapter reviews the discoveries and initial characterizations (1930–1990) of three plant rhabdoviruses, sonchus yellow net virus, potato yellow dwarf virus, and lettuce necrotic yellows virus, that have become model systems for research on this group of enveloped negative-strand RNA plant viruses. We have used our personal perspectives to review the early historical studies of these viruses, the important technologies and tools, such as density gradient centrifugation, that were developed during the research, and to highlight the eminent scientists involved in these discoveries. Early studies on sites of virus replication, virion structure, physicochemical composition, and the use of protoplasts and vector insect cell culture for virus research are discussed, and differences between the nuclear and cytoplasmic lifestyles of plant rhabdoviruses are contrasted. Finally, we briefly summarize the genome organization and more recent developments culminating in the development of a reverse genetics system for plant negative-strand RNA viruses.

Quantitative characterization of soil micro-aggregates: New opportunities from sub-micron resolution synchrotron X-ray microtomography

Soil microaggregates are the fundamental building block, at the micron scale, of the highly hierarchical structure of soils, and can exert a significant control on the local biological metabolism and microbial community partitioning. In this study we propose an analysis protocol for the morphometric characterization of complete soil microaggregates based on sub-micron resolution synchrotron X-ray microtomography. A comprehensive characterization of the aggregate morphology is the first step towards a complete characterization of the soil microaggregates, when trying to correlate morphometric parameters with physical and/or biological properties, or when building models (e.g., effective diffusivity, microbial distribution, etc.). We demonstrate our characterization approach on two single microaggregate samples from dramatically different soil environments: one from Kansas, primarily composed by inorganic particles, and one from Barrow (Alaska) dominated by plant fragments. A series of state-of-the-art morphometric analysis techniques have been employed providing quantitative results highlighting specific differences of the two samples. The role of the microstructure in a scenario microbial population development has been discussed and it has been found that the Barrow microaggregate seems to be more favorable, from a purely geometrical point of view, as also confirmed by a simple model presented in this work. The potential of this approach, when coupled with chemical and biological analysis for a fully comprehensive characterization of soil aggregates in the larger picture of enhanced biological activity, is evident.

Lithostratigraphy of the Pietermaritzburg Formation (Ecca Group, Karoo Supergroup), South Africa

Abstract The Lower Permian Pietermaritzburg Formation is a mudrock-dominated, upward-coarsening stratigraphic unit in the lower Ecca Group (Karoo Supergroup) in the northeastern part of the main Karoo Basin of South Africa. The formation extends over most of the KwaZulu-Natal Province, and due to its lithology and the local climate, it is usually poorly exposed; hence the description is mainly based on borehole records. From a measured thickness of about 430 m south of the type area around Pietermaritzburg, the formation thins progressively northwards and pinches out against the Dwyka Group and pre-Karoo basement north of latitude 26° 30' S. This Lower Permian formation is considered a stratigraphic equivalent of the Prince Albert Formation in the southern part of the main Karoo Basin. The Pietermaritzburg Formation only preserves scattered, fragmentary plant fossil and invertebrate trace fossils, which are diagnostic of marine conditions (e.g. Helminthopsis). Based on its sedimentary facies characteristics and ichnofossil assemblages, the unit was probably deposited under low energy conditions on a northerly shallowing marine shelf that initially experienced deepening (during a major Artinskian transgression) and then shallowing in the early Kungurian.

Guanaco’s diet and forage preferences in Nothofagus forest environments of Tierra del Fuego, Argentina

Aim of study: Guanaco (Lama guanicoe Müller), is a South American native ungulate widely distributed in Patagonia, which in the island of Tierra del Fuego (TF), extends its habitat into Nothofagus spp. forests. Within these forests, guanacos consume lenga (Nothofagus pumilio) leaves and twigs, and other understory species. The aim of this work was to determine: 1) the spring and summer diet of free ranging guanacos, and 2) which plants, grown in the forest understory, guanacos do prefer, or avoid, in these seasons of great forage abundance.Area of study: Tierra del Fuego (Argentina), on three representative areas which combined Nothofagus forests and adjacent meadows (vegas).Material and Methods: Guanacos’ diet was determined by comparing epidermal and non-epidermal plant fragments with micro-histological analyses of feces. The analysis was made from composite samples of fresh feces, collected at the seasons of maximum forage productivity (spring and summer).Main results: During spring, 48% of guanacos’ diet was composed of lenga leaves, 30% of grass-like species, 15% of grasses, and less than 7% of herbs, shrubs, and lichens. In summer, 40% of the diet was composed of grasses, 30% of lenga leaves, 25% of grass-like species and the rest corresponded to herbs, shrubs, and lichens. Within the forest understory, guanaco selected lenga leaves and twigs, grass species were consumed according to their availability (or sometimes rejected), while other herbs were not consumed at all.Research highlights: Guanacos’ consumption preference for lenga, even considering the high availability of other forages, could adversely affect forest regeneration.

Analysis of the plant composition of manatee (Trichechus manatus manatus) faeces in a lake in south‐eastern Mexico

Abstract The Antillean manatee (Trichechus manatus manatus) is a species at risk of extinction. Its diet in freshwater environments has been scarcely studied in Mexico, despite its significance for managing populations and habitat. The diet of Antillean manatees inhabiting the Natural Protected Area of Laguna de las Ilusiones, in Villahermosa, Tabasco, Mexico, was studied during the rainy season. A microhistological analysis was conducted on 51 manatee faecal samples. The cuticle and epidermis of 35 plant species present in vegetation patches used as foraging grounds by the Antillean manatee were described. In total, 223 plant fragments belonging to 11 families and 25 vascular plant taxa were identified. Echinochloa polystachya had the highest frequency (70.6%). Plant richness per faecal sample varied between one and eight plant species. This manatee population feeds mainly on grass. The plant species found coincide with those reported in other studies on sirenian diets. However, 11 new plant species consumed by manatees were recorded. This is the most comprehensive study to date in river systems in Mexico on the botanical richness of manatee faeces. The information provided here can be applied to decision‐making on the conservation of the Antillean manatee and its critical habitat.

Biotic resistance by snails and fish to an exotic invasive aquatic plant

Abstract Hydrilla verticillata (Hydrocharitaceae) is an exotic invasive macrophyte that has caused severe ecological and economic damage worldwide. H. verticillata has invaded the main channel of the river in the Upper Paraná River floodplain (Brazil), but it has not become established in floodplain lakes. Although some abiotic factors have been shown to affect the success of H. verticillata invasions, the role of biotic interactions remains unclear. Here, we set a laboratory experiment investigating how interactions with resident species may influence the success of H. verticillata invasions in floodplain lakes. Based on field observations, we selected three species that represent the most probable ecological interactions negatively impacting the early establishment of H. verticillata: a herbivorous fish (Moenkhausia forestii: Characidae) and herbivorous gastropods in the genus Pomacea (Ampullariidae), both natives, and an exotic shredder fish (Astronotus crassipinnis: Cichlidae). The individual and combined effects of these species on the early phase of H. verticillata establishment were evaluated. The native gastropod had the greatest effect on limiting plant growth due to herbivory, whereas the small native herbivorous fish mostly consumed H. verticillata leaves, and the non‐native shredder fish dislodged the plants from the sediment, preventing their establishment and increasing the number of free propagules (plant fragments) of previously rooted plants. The experimental treatment that combined all three species tended to reduce plant performance descriptors. Our results indicate that biotic resistance may play an important role in reducing the early establishment of H. verticillata in the lakes of this Neotropical floodplain. However, the disturbance caused by the exotic shredder fish may have an undesirable effect at larger scales because it stimulated the production of propagules that may spread to other connected aquatic ecosystems.

Disseminated hyaline ring granuloma in the omentum of a dog

BackgroundHyaline ring granuloma (HRG) is an uncommon histopathologic finding of unsolved etiopathogenesis. According to the exogenous theory, HRG develops due to implantation of foreign material, most probably indigestible plant fragments. HRG is a comparatively rare condition in humans, mostly involving the oral cavity with very rare extraoral locations.Case presentationAn 1-year-old mixed-breed dog in good condition was presented for routine ovariohysterectomy. Disseminated HGR were accidentally found in the omental adipose tissue during surgery. Histopathology revealed the presence of ring-like hyaline structures surrounded by granulomatous inflammation including foreign body-type multinucleated giant cells. The histochemical examinations indicated the exogenous plant origin of the foreign material.ConclusionsThe lesions were similar to the findings in humans with HRG. The definitive diagnosis remains largely based on histopathological examination supported by special histochemical stains. To the best of our knowledge, this is the first case of hyaline ring granuloma reported in a non-human species. Moreover, the omentum is an uncommon location for this condition.

Evaluation of sedimentary processes of plant particles by gravity flow using biomarkers in plant fragment-concentrated sediments of a turbiditic sequence in the Miocene Kawabata Formation distributed along the Higashiyama-gawa River, Yubari, Hokkaido, Japan

Distinctive plant fragment-concentrated sandstones are found in a turbiditic sequence deposited under deep sea environment in the Miocene Kawabata Formation distributed along the Higashiyama-gawa River, Yubari, central Hokkaido, Japan. We observed microscopically the plant fragments and analyzed terrestrial higher plant biomarkers in the sediments to evaluate sedimentological and hydrodynamic behaviors of plant particles by gravity flow depositional processes. Biomarker compositions such as pristane / phytane and regular sterane ratios indicate a large contribution of terrestrial organic matter, especially woody fragments, in the sandstone layer. The relative abundances of terrestrial higher plant terpenoids (pentacyclic triterpenoids, des-A-triterpenoids and diterpenoids) are high in all parts of the sandstone layer, while long-chain n-alkane concentrations are remarkably higher only at the uppermost part. Also, leaf cuticle fragments are mainly found in the uppermost part. These results suggest that plant leaves are mainly deposited in the uppermost part of the sandstone layer. Thus, it is concluded that the variations in plant fragment types (tissues) deposited are thought to be resulted from various hydrodynamic behavior in gravity flow.