| 1. |
- Ahmed, Ajaj, et al.
(författare)
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Evaluation of Thar Desert bacterial lipases for catalytic efficiencies and biodiesel production potentials
- 2023
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Ingår i: Biologia. - : Springer Nature. - 0006-3088 .- 1336-9563. ; 78:4, s. 1187-1197
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Tidskriftsartikel (refereegranskat)abstract
- The present work describes the screening of thermotolerant bacteria isolated from Thar Desert environmental samples for lipase activity and their catalytic efficiencies, such as tolerance to extreme pHs, temperatures, and organic solvents, and efficiency to synthesize biodiesel from waste cooking oils. The selected lipases were thermos-alkaliphilic in nature showing good activity at higher temperatures and in the alkaline pH range with optimal activity at 45 °C and pH 8 or 9. The lipases efficiently converted oils to biodiesel (fatty acid methyl ester), giving up to 78% conversion under specific reaction conditions. The enzyme (lipase) mediated biodiesel production will soon offer an eco-friendly and sustainable energy source for automobiles and industrial applications. The thermos-alkaliphilic properties of these lipases along with their efficiency to produce fatty acid methyl ester from waste cooking oil and methanol as well as other prospective applications, make them potential candidates for biodiesel production and other prospective applications such as the synthesis of flavor and fragrance esters and remediation of various environmental pollutants.
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| 2. |
- Andersson, Michael R., et al.
(författare)
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Mutational analysis of conserved glutamic acids of Pho89, a Saccharomyces cerevisiae high-affinity inorganic phosphate:Na+ symporter
- 2012
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Ingår i: Biologia. - : Springer Science and Business Media LLC. - 0006-3088 .- 1336-9563. ; 67:6, s. 1056-1061
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Tidskriftsartikel (refereegranskat)abstract
- In Saccharomyces cerevisiae, the high-affinity phosphate transport system comprises the Pho84 and Pho89 permeases. The Pho89 permease catalyzes import of inorganic phosphate in a symport manner by utilizing Na+ ions as co-solute. We have addressed the functional importance of two glutamic acid residues at positions 55 and 491. Both residues are highly conserved amongst members of the inorganic phosphate transporter (PiT) family, which might be an indication of functional importance. Moreover, both residues have been shown to be of critical importance in the hPit2 transporter. We have created site-directed mutations of both E55 and E491 to lysine and glutamine. We observed that in all four cases there is a dramatic impact on the transport activity, and thus it seems that they indeed are of functional importance. Following these observations, we addressed the membrane topology of this protein by using several prediction programs. TOPCONS predicts a 7-5 transmembrane segment organization, which is the most concise topology as compared to the hPiT2 transporter. By understanding the functionality of these residues, we are able to correlate the Pho89 topology to that of the hPiT2, and can now further analyze residues which might play a role in the transport activity.
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| 3. |
- Arslan, N., et al.
(författare)
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Aquatic Oligochaeta (Annelida) of Balıkdamı wetland (Turkey), with description of two new species of Phallodrilinae
- 2007
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Ingår i: Biologia. - : Springer Science and Business Media LLC. - 0006-3088 .- 1336-9563. ; 62:3, s. 323-334
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Tidskriftsartikel (refereegranskat)abstract
- The Balıkdamı Wetland, an impoundment of the upper course of the Sakarya River located near Sivrihisar (Eskişehir, Central Anatolia), is one of the most important bird conservation areas in Turkey. This area also encompasses the mouth of the torrential Göksu Stream, which is partly hyporheic. During this study (2001–2003), 1,471 specimens representing 34 taxa of aquatic Oligochaeta were collected from the Balıkdamı Wetland. All the species identified are new records for Balıkdamı. Two species, Coralliodrilus amissus sp. n. and Gianius anatolicus sp. n., are new to science, and five species, Stylodrilus parvus (Hrabě et Černosvitov, 1927), Chaetogaster diastrophus (Gruithuisen, 1828), Peipsidrilus libanus (Giani et al., 1982), Tubifex acuticularis Martinez-Ansemil et Giani, 1983, and Epirodrilus moubayedi Giani et Martinez-Ansemil, 1983, are new records for Turkey. Two other species, Peipsidrilus libanus and Tubifex acuticularis, are re-described. The oligochaete fauna of the wetland was dominated by widely distributed tubificid taxa. The lumbriculid Stylodrilus parvus was the most abundant species in the Göksu stream. The two new phallodriline species are remarkable since most representatives of this subfamily live in the marine environment. Due to the species richness and diversity of Oligochaeta, as well as of several other animal groups, the Balıkdamı wetland area deserves conservation.
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| 4. |
- Brodin, Yngve, et al.
(författare)
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Smaller, lighter coloured and less hairy Procladius (Diptera, Chironomidae) in warmer climate
- 2023
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Ingår i: Biologia. - : Springer Nature. - 0006-3088 .- 1336-9563. ; 78:8, s. 2091-2098
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Tidskriftsartikel (refereegranskat)abstract
- The relationship between body size, colour and hairiness of Procladius of the Diptera family Chironomidae and climate measured as annual mean air temperature was analysed. The study was based on 453 males representing 31 species from 253 localities in 27 countries in Europe and six elsewhere. Wing length as well as three other characters reflecting body size showed significant decrease with warmer climate conditions. The results are in line with several other studies of insects concluding that adult insects are smaller in warmer climate, also considering the implications of global warming. Likewise, all five characters representing colour lightness showed significantly lighter coloured Procladius specimens with warmer climate. The relationship between hairiness and annual mean air temperature was weaker than that of size or colour and temperature, but all five characters studied showed a statistically significant decrease in hairiness with warmer climate. The biological relevance of smaller size, lighter colour and less hairiness in warmer climate can be related to several factors regulating flight and swarming, including less need of protection against cold weather, overheating avoidance, mating success agility and predator escape.
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| 5. |
- Danilov, Roman A, et al.
(författare)
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Periphyton communities on natural substrata in eu-, meso- and oligotrophic lakes at higher latitude
- 2002
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Ingår i: Biologia. - 0006-3088 .- 1336-9563. ; 57:4, s. 433-436
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Tidskriftsartikel (refereegranskat)abstract
- Natural epiphyton and epilithon communities were studied in eu-, meso- and oligotrophic lakes at latitude of 62degrees54' N in Vasternorrlands region of Sweden. The samples of epiphyton as well as epilithon (three per lake) were identical and specific for each lake studied. Both epiphytic and epilithic communities consisted of members of three classes of algae - Cyanophyceae, Chlorophyceae and Bacillariophyceae. The highest species diversity was detected within Chlorophyceae while Cyanophyceae and Bacillariophyceae contained the same amount of species. In general, epiphyton and epilithon shared 44% of species identified. However, both epiphyton and epilithon showed distinct patterns between lakes of different trophic level. Epiphyton in the eutrophic lakes were clearly dominated by Cyanophyceae (Bacillariophyceae co-dominated in one of the eutrophic lakes). Both mesotrophic and oligotrophic lakes were signed by high abundance of Chlorophyceae and almost complete absence of Bacillariophyceae and Cyanophyceae. Epilithic communities in the oligotrophic lakes had higher species diversity than those in the meso- and eutrophic lakes studied. Chlorophyceae were dominant in two eutrophic lakes and Cyanophyceae only in one eutrophic lake, Chlorophyceae as well as Bacillariophyceae were abundant in the oligotrophic lakes. Cluster analysis based on species presence-absence led to a sufficient resolution between both epiphytic and epilithic communities of eutrophic environments, on the one hand, and epiphytic and epilithic communities of meso- and oligotrophic environments, on the other.
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| 6. |
- Danilov, Roman, et al.
(författare)
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Effects of copper on growth rate, cell shape, motility and photosynthesis in the green flagellate Euglena gracilis in a long-term experiment
- 2000
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Ingår i: Biologia. - 0006-3088 .- 1336-9563. ; 55:4, s. 413-418
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Tidskriftsartikel (refereegranskat)abstract
- The green flagellate Euglena gracilis was treated for seven days with concentrations of copper ranging from 0.02 mg L-1 to 2.0 mg L-1. No inhibiting effects were detected in any physiological parameters measured. In general, it seems that enhanced copper concentrations stimulated photosynthetic efficiency (PE) of E. gracilis. Concentrations of copper reported to be critical for the other algae studied (from 0.10 mg L-1 to 0.14 mg L-1) did not show any severe negative effects on E. gracilis. An unusual trend was observed where an increase in PE was followed by an increase in light irradiance necessary to achieve light compensation point. High capacity of E. gracilis to adapt to copper stress is being discussed as a possible explanation for the trends detected.
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| 7. |
- Eckstein, Rolf Lutz, et al.
(författare)
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Variation in life-cycle between three rare and endangered floodplain violets in two regions : implications for population viability and conservation
- 2009
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Ingår i: Biologia. - : Springer Science and Business Media LLC. - 0006-3088 .- 1336-9563. ; 64:1, s. 69-80
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Tidskriftsartikel (refereegranskat)abstract
- We studied the demography of Viola elatior, V. pumila, and V. stagnina, three rare and endangered Central European floodplain species, to (i) analyse variation in life-cycles among congeners and between regions (Dyje-Morava floodplains, Czech Republic; Upper Rhine, Germany), (ii) to define sensitive stages in the life-cycles, and (iii) to identify possible threats for population viability and species conservation. Matrix models were based on the fate of marked individuals from a total of 27 populations over two years. We analysed population growth rate (lambda), stage distribution, net reproductive rate (R (0)), generation time, age at first reproduction, and elasticity and calculated a life table response experiment (LTRE). Most populations were declining and lambda did not differ between species or regions during the observed interval. Despite higher probabilities for survival and flowering in the Dyje populations, R (0) was higher in the Rhine populations. Also other demographic traits showed consistent differences between regions and/or species. Complex life-cycles and large variation in lambda precluded unequivocal identification of sensitive stages or vital rates for conservation. Variation between regions may be a consequence of differences in habitat quality. Our results suggest that deterministic processes such as reduced management, succession, habitat destruction, and lack of disturbance through reduced or eliminated flooding present the strongest threat for the viability and persistence of populations of the three floodplain violets as compared with stochastic processes. However, the persistent seed bank of the species may buffer populations against environmental variation and represents a reservoir for recovery after resumption of suitable land-use management.
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| 8. |
- Ekelund, Nils, 1956-, et al.
(författare)
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Effects of autumnal stratification on phytoplankton communities in Lake Solumsjö, Sweden: Application of diversity indices and multivariate methods
- 2000
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Ingår i: Biologia. - 0006-3088 .- 1336-9563. ; 55:4, s. 357-362
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Tidskriftsartikel (refereegranskat)abstract
- Effects of autumnal stratification on phytoplankton communities at different depths were studied in Lake Solumsjö, NE Sweden. Species number, Shannon-Weaver’s, Margalef’s and Menhinick’s indices as well as cluster analyses using presence-absence with abundance matrices were applied. All diversity indices used clearly indicated higher diversity in epilimnion compared to that in hypolimnion. This pattern can be explained by sole dominance of Trachelomonas volvocinopsis under predominantly anoxic conditions and high concentrations of iron and manganese below the thermal gradient. Stratification disappeared between September 29 and October 4, thus leading to homogenisation of water column and similar phytoplankton communities at all depths. Cluster analyses using presence-absence with abundance matrices turned out to be a powerful tool when studying temporal changes in phytoplankton communities as a result of stratification patterns. Two distinct clusters at depths of 0, 2 and 10 m were clearly separated: one containing algal communities during stratification and one containing algal communities after the thermal gradient disappeared. At the depth of 5 m more homogeny between phytoplankton communities under stratified and mixed conditions was observed.
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| 9. |
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| 10. |
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| 11. |
- Jiang, W., et al.
(författare)
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Genetic and morphological analyses uncover a new record and a cryptic species in Allonais (Clitellata: Naididae)
- 2021
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Ingår i: Biologia. - : Springer Science and Business Media LLC. - 0006-3088 .- 1336-9563. ; 76:6, s. 1705-1714
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Tidskriftsartikel (refereegranskat)abstract
- Allonais inaequalis (Stephenson, 1911) is a well-known "morpho-species" of the subfamily Naidinae with a wide distribution in the world. In this study we describe it, as a new record, from China, and we compare molecular data of A. inaequalis from two geographic populations in China and one in Peru, and we re-evaluate the phylogenetic status of Allonais. Sequence data of both mitochondrial (COI, 12S rDNA and 16S rDNA) and nuclear (18S rDNA and 28S rDNA) from 26 species of naidids (representing 14 of the 22 genera currently recognized) and 7 outgroup taxa were used. The combined data set were analyzed with Bayesian inference and Maximum Likelihood. The different phylogenetic analyses gave largely congruent trees, and they corroborate monophyly of Allonais. The results show that the genetic distances among the three geographic populations of A. inaequalis for COI are 0.0%-7.8% and for 28S vary between 0.0% and 0.8%. Allonais inaequalis falls into two groups, one from China, and one from Peru. We suggest that the Chinese morphotype more resembles A. inaequalis from India, where the species was first described, whereas the species in Peru is likely to be another species.
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| 12. |
- Krecek, Josef, et al.
(författare)
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Hydrological processes in small catchments of mountain headwater lakes : The Tatra Mountains
- 2006
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Ingår i: Biologia. - 0006-3088 .- 1336-9563. ; 61, s. S1-S10
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Tidskriftsartikel (refereegranskat)abstract
- This study evaluates runoff and different methods for the estimation of water balance and runoff genesis in four small alpine catchments, which lie outside the standard network of hydrological and climate networks. These test catchments, whose size ranges between 2.3 and 110 ha, are located above the timberline at elevations between 1,784 and 2,380 m. Their land surfaces consist of lakes, rock formations, debris deposits, and alpine meadows. Hydrological data were collected for the water year 2001. The catchments were instrumented by three automatic weather stations recording global and net solar radiation, air temperature, humidity, precipitation, and soil temperature. Lake water levels were registered with staff gauges and runoff evaluated from water storage calculations. Runoff genesis was investigated by means of chemical tracers (Rhodamine WT and Lithium chloride). Hydrological process estimations were made using standard methods including: the input of precipitation and snowmelt, both potential and actual evaporation, which was estimated by the approaches of HAMON, PRIESTLEY-TAYLOR, PENMAN and GRINDLEY, and runoff calculated from the lake storage, were compared with results of the conceptual hydrological BROOK90 model. The empirical results show that hydrological processes are governed by the temperature-dependent regime of high mountain snowmelt. However, the major differences in water yield and runoff genesis between watersheds were due to differences in the morphologies of the lakes and their basins, the soil-vegetation complex, and runoff routing. Evaluating approaches to estimation, PENMAN's combination of both aerodynamic and energy balance method provides the best fit to observed data with observed evapotranspiration being 78 to 99% of the potential calculated. The deterministic BROOK90 model is effective for precipitation-runoff genesis studies in small headwater catchments. In the L'adove pleso basin predicted and observed water yield show close correlation. The annual sum of actual evapotranspiration calculated by BROOK90 (352 mm) corresponds closely to that estimated by the approach of Penman (386 mm).
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| 13. |
- Larsbo, Mats, et al.
(författare)
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Effects of surfactant use and peat amendment on leaching of fungicides and nitrate from golf greens
- 2009
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Ingår i: Biologia. - : Springer Science and Business Media LLC. - 0006-3088 .- 1336-9563. ; 64, s. 419-423
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Tidskriftsartikel (refereegranskat)abstract
- Soil water repellency in golf putting greens may induce preferential "finger flow", leading to enhanced leaching of surface applied agrochemicals such as fungicides and nitrate. We examined the effects of root zone composition and the use of the non-ionic surfactant Revolution on soil water repellency, soil water content distributions, infiltration rates, turf quality, and fungicide and nitrate leaching from April 2007 to April 2008. The study was made on 4-year-old experimental green seeded with creeping bentgrass (Agrostis stolonifera L.) 'Penn A-4' at Landvik in southeast Norway. Eight lysimeters with two different root zone materials: (i) straight sand (1% gravel, 96% sand, 3% silt and clay, and 4 g kg(-1) organic matter) (SS) and (ii) straight sand mixed with Sphagnum peat to an organic matter content of 25 g kg(-1) (SP) were used in this study. Surfactant treatment reduced the spatial variability of water contents, increased infiltration rates and reduced water drop penetration times (WDPTs) by on average 99% in and just below the thatch layer. These effects were most evident for SS lysimeters. Surfactant treatment resulted on average in an 80% reduction of total fungicide leaching, presumably due to reduced preferential finger flow facilitated by decreased soil water repellency. Peat amendment reduced fungicide leaching by 90%, probably due to increased sorption of the fungicides to organic matter. Nitrate leaching was also smaller from surfactant-treated straight-sand root zones, but this effect was not significant.
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| 14. |
- Nahalkova, Jarmila, et al.
(författare)
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Lectin-like activity in European black pine (Pinus nigra) seed protein bodies
- 1999
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Ingår i: Biologia. - 0006-3088 .- 1336-9563. ; 54:1, s. 113-117
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Tidskriftsartikel (refereegranskat)abstract
- A study of black pine seed protein bodies with regard to the presence of defense-related proteins was performed. Interaction of the intact protein bodies with saccharides revealed specificity of surface membrane binding sites for chitin, cellulose, laminarin and the respective mono- or disaccharides. Crude protein fraction isolated from protein bodies possessed an ability to agglutinate fungal spores. Inhibiton of the fungal spores agglutination confirmed the presence of lectin-like proteins specific to basic fungal cell wall components.
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| 15. |
- Nahar, Noor, et al.
(författare)
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Functional studies of AtACR2 gene putatively involved in accumulation, reduction and/or sequestration of arsenic species in plants
- 2017
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Ingår i: Biologia. - : Walter de Gruyter. - 0006-3088 .- 1336-9563. ; 72:5, s. 520-526
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Tidskriftsartikel (refereegranskat)abstract
- Food-based exposure to arsenic is a human carcinogen and can severely impact human health resulting in many cancerous diseases and various neurological and vascular disorders. This project is a part of our attempts to develop new varieties of crops for avoiding arsenic contaminated foods. For this purpose, we have previously identified four key genes, and molecular functions of two of these, AtACR2 and AtPCSl, have been studied based on both in silico and in vivo experiments. In the present study, a T-DNA tagged mutant, (SALK-143282C with mutation in AtACR2 gene) of Arabidopsis thaliana was studied for further verification of the function of AtACR2 gene. Semi-quantitative RT-PCR analyses revealed that this mutant exhibits a significantly reduced expression of the AtACR2 gene. When exposed to 100 μM of arsenate (AsV) for three weeks, the mutant plants accumulated arsenic approximately three times higher (778 μg/g d. wt.) than that observed in the control plants (235 μg/g d. wt.). In contrast, when the plants were exposed to 100 μM of arsenite (AsIII), no significant difference in arsenic accumulation was observed between the control and the mutant plants (535 μg/g d. wt. and 498 μg/g d. wt., respectively). Also, when arsenate and arsenite was measured separately either in shoots or roots, significant differences in accumulation of these substances were observed between the mutant and the control plants. These results suggest that AtACR2 gene is involved not only in accumulation of arsenic in plants, but also in conversion of arsenate to arsenite inside the plant cells. © 2017 Institute of Molecular Biology, Slovak Academy of Sciences.
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| 16. |
- Nawani, Neelu, et al.
(författare)
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Status of metal pollution in rivers flowing through urban settlements at Pune and its effect on resident microflora
- 2016
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Ingår i: Biologia. - Bratislava : Springer. - 0006-3088 .- 1336-9563. ; 71:5, s. 494-507
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Tidskriftsartikel (refereegranskat)abstract
- This study illustrates the sporadic distribution of metals in fluvial systems flowing from catchments to urban settlements. This is a detailed study prognosticating the deteriorating quality of rivers at specific locations due to metal pollution. Heavy metals like cadmium, lead, nickel and mercury are prominent in industrial sector. Contour plots derived using spatial and temporal data could determine the focal point of metal pollution and its gradation. Metal values recorded were cadmium 157 mg/L, lead 47 mg/L, nickel 61 mg/L and mercury 0.56 mg/L. Prokaryote diversity was less in polluted water and it harboured metal tolerant bacteria, which were isolated from these polluted sites. Actinomycetes like Streptomyces and several other bacteria like Stenotrophomonas and Pseudomonas isolated from the polluted river sites exhibited changes in morphology in presence of heavy metals. This stress response offered remedial measures as Streptomyces were effective in biosorption of cadmium, nickel and lead and Stenotrophomonas and Pseudomonas were effective in the bioaccumulation of lead and cadmium. The amount of 89 mg of lead and 106 mg of nickel could be adsorbed on one gram of Streptomyces biomass-based biosorbent. Such biological remedies can be further explored to remove metals from polluted sites and from metal contaminated industrial or waste waters.
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| 17. |
- Nordberg Karlsson, Eva, et al.
(författare)
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Differences and similarities in enzymes from the neopullulanase subfamily isolated from thermophilic species
- 2008
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Ingår i: Biologia. - : Springer Science and Business Media LLC. - 0006-3088 .- 1336-9563. ; 63:6, s. 1006-1014
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Konferensbidrag (refereegranskat)abstract
- Six glycoside hydrolase (GH) family 13 members, classified under the polyspecific neopullulanase subfamily GH13_20 (also termed cyclomaltodextrinase) were analysed. They originate from thermophilic bacterial strains (Anoxybacillus flavithermus, Laceyella sacchari, and Geobacillus thermoleovorans) or from environmental DNA, collected after in situ enrichments in Icelandic hot springs. The genes were isolated following the CODEHOP consensus primer strategy, utilizing the first two of the four conserved sequence regions in GH13. The typical domain structure of GH13 20, including an N-terminal domain (classified as CBM34), the catalytic module composed of the A- and B- domains, and a C- terminal domain, was found in five of the encoded enzymes (abbreviated Amy1, 89, 92, 98 and 132). These five enzymes degraded cyclomaltodextrins (CDs) and starch, while only three, Amy92 (L. sacchari), Amy98 (A. flavithermus) and Amy132 (environmental DNA), also harboured neopullulanase activity. The L. sacchari enzyme was monomeric, but with CD as the preferred substrate, which is an unusual combination. The sixth enzyme (Amy29 from environmental DNA), was composed of the ABC-domains only. Preferred substrate for Amy29 was pullulan, which was degraded to panose, and the enzyme had no detectable activity on CDs. In addition to its different activity pro. le and domain composition, Amy29 also displayed a different conservation (LPKF) in the fifth conserved region (MPKL) proposed to identify the subfamily. All enzymes had apparent temperature optima in the range 50-65 degrees C, while thermostability varied, and was highest for Amy29 with a half-life of 480 min at 80 degrees C. Calcium dependent activity or stability was monitored in four enzymes, but could not be detected for Amy29 or 98. Tightly bound calcium can, however, not be ruled out, and putative calcium ligands were conserved in Amy98.
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| 18. |
- Salgaonkar, Neeta A., et al.
(författare)
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Use of N,N-diacetylchitobiose in decreasing toxic effects of indoor air pollution by preventing oxidative DNA damage
- 2016
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Ingår i: Biologia. - Bratislava : Springer. - 0006-3088 .- 1336-9563. ; 71:5, s. 505-515
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Tidskriftsartikel (refereegranskat)abstract
- Indoor air pollution occurs due to hazardous pollutants, such as tobacco smoke, pesticides and carbon oxides, sulphur oxides and nitrogen oxides arising from combustion of biomass fuels. Exposure to these pollutants results in respiratory conditions like asthma, chronic obstructive pulmonary disease, lung cancer, pneumonia and other lower respiratory infections. Several of these infections are a result of inflammation and oxidative stress. Here we demonstrate the ability of N,N-diacetylchitobiose in preventing oxidative DNA damage in peripheral blood mononuclear cells exposed to biomass smoke extracts and cigarette smoke extract. The cytotoxic effect of these pollutants was determined by trypan blue exclusion assay in peripheral blood mononuclear cells, where cytotoxicity in decreasing order was garette > wood > sawdust > cowdung. Cytotoxicity could be due to single- and double-strand breaks in the DNA as a result of oxidative stress. Comet assay measures the extent of DNA damage in the cells exposed to toxic agents. When mononuclear cells were treated with N,N-diacetylchitobiose and later exposed to smoke extracts, the extent of DNA damage decreased by 44.5% and 57.5% as compared to untreated cells. The protection offered by N,N-diacetylchitobiose towards oxidative DNA damage was at par with quercetin, a popular herbal medicine. Glutathione-S-transferase activity was determined in mononuclear cells exposed to smoke extracts, where oxidative stress in cells exposed to cigarette smoke extract was maximum. The present study demonstrates for the first time the ability of N,N -diacetylchitobiose to alleviate the harmful effects of indoor air pollutants.
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| 19. |
- Srinivasan, Sivabalan, et al.
(författare)
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On the identity and phylogenetic position of Dero indica (Clitellata: Naididae)
- 2020
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Ingår i: Biologia. - : Springer Science and Business Media LLC. - 0006-3088 .- 1336-9563. ; 75, s. 1685-9
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Tidskriftsartikel (refereegranskat)abstract
- The identity and validity of the freshwater worm Dero indica (Clitellata: Naididae; Naidinae) has been debated, and it has been suggested that it is likely to be identical with D. digitata. In this study we combine a newly generated COI sequence of D. indica with available sequences from GenBank, to estimate the phylogeny of Dero using both Bayesian Inference and Maximum Likelihood. The trees show that D. indica is well separated from D. digitata, instead it isclosest to D. vaga, but with low support. Furthermore, the analyses confirm the close relationship between Dero and Branchiodrilus found in previous studies, and indicates the presence of cryptic species in D. furcata and D. digitata.
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| 20. |
- Sunny, Jithin S., et al.
(författare)
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Converting the genomic knowledge base to build protein specific machine learning prediction models; a classification study on thermophilic serine protease
- 2022
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Ingår i: Biologia. - : Springer Science and Business Media LLC. - 0006-3088 .- 1336-9563. ; 77:12, s. 3615-3622
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Tidskriftsartikel (refereegranskat)abstract
- Several machine learning models have been formulated for protein classification based on an important prerequisite for industrial usage, thermostability, and described herein a classification model for a specific enzyme; serine protease. For building the classifier, 283 thermophilic and 200 mesophilic bacterial genomes were mined for their respective serine protease sequences. Features were extracted from 760 sequences, followed by feature selection. We deployed a random forest-based classifier that identified thermophilic and non-thermophilic serine proteases with an accuracy of 97.11%, higher than other benchmark machine learning methods. Knowledge of thermostability and amino acid positional shifts can be vital for downstream protein engineering techniques. Thus, a web platform has been proposed to emphasize the real-time application of this enzyme-specific classification model. We designed a framework that can aid protein engineers in combining their sequence data and the classification model and employ it to align query sequences against the custom databases and identify similar novel enzymes along with their thermophilic nature.
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| 21. |
- Vookova, B, et al.
(författare)
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Defense reaction of pine seeds : distribution of protein bodies extract from Pinus nigra seeds in agar medium plates
- 1999
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Ingår i: Biologia. - 0006-3088 .- 1336-9563. ; 54:1, s. 107-111
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Tidskriftsartikel (refereegranskat)abstract
- Diffusion and distribution of protein bodies (PB) extract from Pinus nigra seeds in agar medium plates was studied. After application of PB extract on filter paper discs it was placed on agar plates for 20 days. Proteins diffused from the discs were distributed in the plates. Identical protein pattern (8-54 kDa molecules) of PB extract was defined by SDS-PAGE analysis in agar strips at different distances from the discs. The predominant peptides and proteins were 8, 9, 13 and 18 kDa. The 32-36 kDa proteins were absent. These results suggest that the proteins during the maintenance on agar medium plates were separated. Relative quantity of individual proteins was different in certain distances from the discs. It is probable that these proteins can be involved in defense of pine megagametophyte. We assume that proportion of individual proteins is also of importance in their defense function.
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| 22. |
- Zidarova, Ralitsa, et al.
(författare)
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Karyological and endosymbiotic notes on two Choricystis species (Trebouxiophyceae, Chlorophyta)
- 2009
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Ingår i: Biologia. - : Springer Science and Business Media LLC. - 0006-3088 .- 1336-9563. ; 64:1, s. 43-47
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Tidskriftsartikel (refereegranskat)abstract
- Two species of the genus Choricystis (Choricystis minor and Choricystis chodatii) have been chromosomally surveyed. In addition, their ability to form symbiotic associations with the ciliate Paramecium bursaria was also investigated. Choricystis minor (clone #8931/1 from strain #8931) was isolated from a moss sample collected on Livingston Island, Maritime Antarctica. Choricystis chodatii (clone #3090/1) was derived from strain #3090 Chodat-type culture (loc. Switzerland, lake Geneva). The karyotypes of both species showed a haploid number of five chromosomes and shared some similarity in the chromosome lengths. The absolute chromosome lengths ranged from 1.25 A mu m to 2.95 A mu m. Studied species possess equal abilities for endosymbiotic associations with Paramecium bursaria. Descriptions of the species and a short discussion on their taxonomical status are given.
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| 23. |
- Turner, Pernilla, et al.
(författare)
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Monomeric and dimeric cyclomaltodextrinases reveal different modes of substrate degradation
- 2005
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Ingår i: Biologia. - 0006-3088. ; 60:Suppl. 16, s. 79-87
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Tidskriftsartikel (refereegranskat)abstract
- Two cyclomaltodextrinases (CDase) of thermophilic origin were investigated for their action on cyclodextrins. Although most CDases known today are made up of at least homodimers, one of the enzymes studied was shown to be a monomer in solution, while the other one was a dimer. Interestingly, the dimeric enzyme had a much superior selectivity for a cyclodextrin substrate compared to its monomeric homologue, with a specific activity on α-cyclodextrin around 100 times higher than for the polymeric substrates starch and pullulan. Moreover, the monomeric CDase had a 10 times higher activity on those polymers than the dimer. The degradation pattern on cyclodextrins was examined by high-performance anion-exchange chromatography in combination with microdialysis. The final products were almost exclusively maltose and glucose in an approximate molar ratio of 2:1. However, the intermediate product ratios were quite different for the two enzymes, revealing that the monomeric CDase had a more random distribution of transitional products. Moreover, the dimeric CDase accumulated maltotriose, which is believed to be due to transglycosylation. The oligomeric state of the enzymes is thought to be a key factor for exhibiting high cyclodextrinase as well as transglycosylation activity.
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| 24. |
- Hadzidimitriou, Anastasia, et al.
(författare)
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Is there a role for antigen selection in mantle cell lymphoma? : Immunogenetic support from a series of 807 cases
- 2011
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Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 118:11, s. 3088-3095
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Tidskriftsartikel (refereegranskat)abstract
- We examined 807 productive IGHV-IGHD-IGHJ gene rearrangements from mantle cell lymphoma (MCL) cases, by far the largest series to date. The IGHV gene repertoire was remarkably biased, with IGHV3-21, IGHV4-34, IGHV1-8, and IGHV3-23 accounting for 46.3% of the cohort. Eighty-four of 807 (10.4%) cases, mainly using the IGHV3-21 and IGHV4-34 genes, were found to bear stereotyped heavy complementarity-determining region 3 (VH CDR3) sequences and were placed in 38 clusters. Notably, the MCL stereotypes were distinct from those reported for chronic lymphocytic leukemia. Based on somatic hypermutation (SHM) status, 238/807 sequences (29.5%) carried IGHV genes with 100% germ line identity; the remainder (569/807; 70.5%) exhibited different SHM impact, ranging from minimal (in most cases) to pronounced. Shared replacement mutations across the IGHV gene were identified for certain subgroups, especially those using IGHV3-21, IGHV1-8, and IGHV3-23. Comparison with other entities, in particular CLL, revealed that several of these mutations were "MCL-biased." In conclusion, MCL is characterized by a highly restricted immunoglobulin gene repertoire with stereotyped VH CDR3s and very precise SHM targeting, strongly implying a role for antigen-driven selection of the clonogenic progenitors. Hence, an antigen-driven origin of MCL could be envisaged, at least for subsets of cases.
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