Miracle-dz/UniFAR-FTUs huggingface dataset:
The relationship between N, P returned via litter production and nutrient use efficiency of heath and peat swamp forests in Central Kalimantan

The study of nutrient use efficiency in a heath and a peat swamp forest was carried out in Palangkaraya, Central Kalimantan. There was a stronger correlation in the heath forest between nitrogen and phosphorus in above ground litterfall than in the peat swamp forest, and higher positive correlation between litterfall mass and nitrogen return via litterfall in the heath than in the peat swamp forest, compared to phosphorus. The heath forest used nutrient more efficiently than the peat swamp forest and thus was more efficient in retranslocating nutrients. This phenomenon is important for plants to adapt to the heath forest conditions. Both the heath and peat swamp forests in this study were more efficient in their nutrient use than the mixed dipterocarp forests. There was a specific pattern of NUEP (phosphorus used efficiency): the NUEP was higher when P in litterfall was low, suggesting a seasonal effect. Thus in the heath and peat swamp forests, plants use interesting and important nutrient use strategy to adapt to seasonal change.
Inhibitor of virus replication from protoplasts of a hypersensitive tobacco cultivar infected with tobacco mosaic virus is associated with a 23-K protein species.

(.) Electroeluted protein from SDS-PAGE gels was biologically active, with about a 20-fold increase in specific activity over that of the crude preparation. The active fraction revealed only one protein band at 23 K in PAGE, providing evidence that the 23-K protein is IVR purified to a high degree. A homologous antiserum to the 23-K protein was prepared. The antiserum was highly specific for IVR and efficiently eliminated its antiviral activity. Western blots of IVR extracted from protoplasts or leaf tissue of hypersensitive tobacco cultivar revealed a single 23-K protein band
Assessment of RAPD variation in Abies nebrodensis (Lojac.) Mattei (Pinaceae) using haploid tissue analysis

RAPD technique using haploid DNA from megagametophyte tissue was applied to detect the pattern of genetic variation within Abies nebrodensis, a species endemic to Sicily. Results were compared with a reference system composed of representatives of five Mediterranean firs: A. alba, A. cephalonica, A. nordmanniana, A. numidica, and A. pinsapo. Diploid genotypes for RAPD loci were inferred from segregation patterns in haploid megagametophytes from individual trees. Therefore, it was possible to distinguish between homo- and heterozygotes carrying a RAPD fragment and to calculate unbiased estimates of genetic parameters. In the interspecific comparison, A. nebrodensis appears intermixed with the other Abies species, supporting the hypothesis of remarkable hybridization processes within the genus. A high level of polymorphism and deviation from panmictic equilibrium as a result of heterozygote excess depict a pattern of population structure in A. nebrodensis that agrees with the expectations for an outcrossing perennial species, in spite of its critical conditions. Implications with respect to the conservation management of the species are also discussed.
Reproductive patterns of European pond turtles differ between sites: a small scale scenario

From 1996 to 2002, we studied the body size, measures of reproductive strategy (relative clutch mass and delayed reproduction at sexual maturity), and reproductive output (clutch frequency and annual egg production) of female European Pond turtles, Emys orbicularis , at two sites separated by 12 km in central Mediterranean Tuscany (San Rossore and Camp Darby, central northern Italy). Females did not reproduce at the first appearance of external sexual characters, but reproduced at larger sizes, probably as older turtles. Among years, reproductive females were more common than were non-reproductive females, yet both groups had similar body sizes. Body size (carapace length and width, plastron length and width, shell height and body mass) varied between localities and among years. Body size differed between reproductive and non reproductive females in Camp Darby, but not in San Rossore females. Shell volume did not vary among years, nor between localities, nor between reproductive status. Reproductive females had higher body condition indices (BCI) than did non-reproductive females, while BCI did not differ between females laying one clutch and females laying multiple clutches. Clutch size did not vary among years. One clutch per year was much more frequent than multiple clutches, and multiple clutches were more frequent in Camp Darby than in San Rossore females, likely due to differences in population structures between sites.
Molecular dynamics and Conformational flexibility in Heat Shock Protein 60.2 of Mycobacterium tuberculosis

HSP 60.2 plays important role in pathogenesis of Mycobacterium tuberculosis causing tuberculosis. This chaperonin comprises of three domains namely-apical, intermediate and equatorial which assists in proper protein folding thus preventing aggregation of unfolded polypeptides. To evaluate the structural changes during protein folding, conformations of HSP 60.2 were monitored during 10 ns time scale. Molecular dynamic simulations are used to study the large amount of molecular and biomolecular conformations with the use of high end computational assistance. The Principal component analysis and clustering techniques are used for revealing major conformational changes that occur in the MD simulation. Normal mode analysis was also performed to study the conformation and direction of motion of a protein under study for a large time scale simulation. These studies suggest that functional behavior of protein that depends on the structure. Chaperonin 60.2 is not only plays a role as protein folding machinery, but also an immunologically important biomolecule. Hence it is provided and drawn a clear path between role of chaperon in protein folding and their role in the infection showing the immunological importance of Heat Shock Protein 60.2.
Trafficking Regulation and Energetics

Growing evidence support the idea that impairments in Fast Axonal Transport (FAT) play a crucial role in Neurodegenerative Diseases (NDs). Huntington’s Disease is neurodegenerative disorder caused by an abnormal polyglutamine expansion in the N-Terminal part of huntingtin (HTT), a large scaffold protein implicated in transport regulation. Both the presence of the mutated HTT as the loss of HTT leads to transport defects in mammals. In the fruit fly overexpression of the mutant HTT recapitulates the phenotype observed in mammals. However, it is still unclear whether HTT’s function is conserved in D. melanogaster. Here, we show that D. melanogaster HTT (DmHTT) associates with vesicles, microtubules, and interacts with dynein. In rat cortical neurons, DmHTT partially replaces mammalian HTT in fast axonal transport, and DmHTT KO flies show axonal transport defects in vivo. These results suggest that HTT function in transport is conserved in D. melanogaster.FAT is a process that requires a constant supply of energy. Mitochondria are the main producers of ATP in the cell. However, we have demonstrated that FAT does not depend on this source of energy, as previously thought, but it depends on glycolytic ATP produced on vesicles. Perturbing GAPDH or PK, the two ATP generating glycolytic enzymes, slows down vesicular transport. However, knocking down GAPDH does not affect mitochondrial transport. Furthermore, all of the glycolytic enzymes are associated with dynamic vesicles, and are capable of producing their own ATP. Finally, we show that this ATP production is sufficient to sustain their own transport, demonstrating the energetical autonomy of vesicles for transport.
Genetic structure and diversity of squids with contrasting life histories in the Humboldt Current System

Dosidiscus gigas and Doryteuthis gahi are the most abundant squids in the Humboldt Current System (HCS). These species have contrasting life histories. To determine the genetic structure and diversity of these species, we collected samples from different places in the HCS and amplified a fragment of the mitochondrial cytochrome C oxidase I gene. The molecular analysis of D. gigas revealed low genetic diversity, absence of population structure and evidence for a demographic expansion during the transition from the last glacial period to the current interglacial. These results suggest that D. gigas is composed of one large population with high levels of gene flow throughout the HCS. In the case of D. gahi, the sequences indicated the presence of two population units in the HCS, one in south-central Chile and one in Peru. The Chilean unit had greater genetic diversity, suggesting that it is an old, relatively stable population. In the Peruvian unit there was less genetic diversity and evidence of a recent demographic expansion. The changes in distribution ranges and population sizes of the squid populations may be related to historical variations in productivity along the HCS. The different dispersion and migration capacities of these species may explain the differences in their structure; however, the genetic diversity of both species appears to be more related to historical variations in their distribution ranges and the biogeographic origin of each.
Fetal growth of northern fur seals: life-history strategy and sources of variation

Sex-specific growth curves are described for northern fur seal fetuses, Callorhinus ursinus. The relationships between body length, body mass, and gestational age are derived by regression analysis based on 7000 fetuses collected during 1958–1974 as part of a joint Canadian–American pelagic research effort. Male fetuses grow faster and larger than female fetuses. Length approaches an asymptote with time, but the increase in fetal mass appears exponential until parturition. The size of the fetus is influenced by the age, size, and reproductive history of the mother. Primiparous females produce smaller pups than multiparous females. This difference in fetal size is presumably due to physiological changes associated with having been previously pregnant and is not explained merely by differences in the size and age of the different parities. Older and larger females produce progressively larger fetuses until reaching their reproductive prime at about the age of 10–11 years. Adult females continue to grow beyo.
Chasing sympatric speciation: The relative importance and genetic basis of prezygotic isolation barriers in diverging populations of Spodoptera frugiperda

This thesis investigates the mechanisms underlying three prezygotic isolation barriers between the corn- and the rice-strain of the noctuid moth Spodoptera frugiperda to determine possible interactions between these isolation barriers and their relative importance for sympatric speciation. First, we investigated the role of host plant differentiation as isolation barrier between the two strains. Our analysis shows that, although there is some host-associated genetic structure, host plant differentiation alone cannot explain the total genetic variance and thus other, additional factors must maintain the genetic differentiation. Second, we focused on differentiation in sexual communication between the two strains. Females emit a strain-specific sex pheromone blend, but males do not show a preference for the blend of their own strain. The third and most consistent prezygotic isolation barrier between the two strains is allochronic differentiation, i.e. the strains differ in the daily timing of their sexual activities. We found one major QTL for the circadian differentiation, the circadian clock gene vrille maps to this locus, which is thus the major candidate gene underlying this circadian differentiation. Finally, I discuss the evolutionary potential of the different isolation barriers and I propose an interaction between all prezygotic mating barriers which facilitate the divergence of the two strains, with allochronic differentiation being the driving force. In conclusion, by investigating the prezygotic isolation barriers between two sympatric strains of S. frugiperda in detail, I have determined their strengths and possible interactions, giving insights in the mechanisms underlying and facilitating the process of sympatric speciation.
Acetogenic Bacteria Mainly Contribute to the Disposal of Hydrogen in the Colon of Healthy Japanese

Hydrogen-utilizing bacteria in the feces of Japanese individuals were analyzed with the specific polymerase chain reaction targeting the functional genes. The formyltetrahydrofolate synthetase gene derived from acetogenic bacteria was predominantly detected in all subjects. We consider that reductive acetogenesis might be an important H 2 disposal pathway in healthy Japanese.
The Asian Umbelliferae Biodiversity Database (ASIUM) with Particular Reference to South-West Asian Taxa

An original database, ASIUM, on Asian Umbelliferae has been compiled at the Moscow State University to include all accepted names and synonyms, principal citations in regional Floras, monographs and critical articles, protologue data and distribution in countries, their regions and provinces. A special option permits the arrangement of synomyms, which can be divided into several homotypic groups. It is also possible to extract information for analysis and comparison, for instance, of species sets from different regions to estimate their similarity. ASIUM is a mobile monograph of the Umbelliferae for a continent, with their maximal biodiversity at the generic and specific levels: 286 genera and 2089 species of the family (s.l.) are registered in the database. The largest Umbelliferae genera in Asia are Ferula L. , Bupleurum L. , Pimpinella L. , Heracleum L. , Seseli L. , Angelica L. , Bunium L. , Prangos Lindl. , Ferulago W.D. J.Koch, Hymenidium Lindl. , Hydrocotyle L. , Chaerophyllum L. , Eryngium L. , Pternopetalum Franch. , Elaeosticta Fenzl, Acronema Falc. ex Edgew. and Semenovia Regel & Herder. Maximal species diversity is observed in China, Asiatic Turkey, Iran, Asiatic Russia, Kazakhstan, India, Afghanistan, Kyrgyzstan, Uzbekistan, Georgia and Syria. Nearly all these countries boast the largest number of endemics. In Turkey there are 4 endemic genera and 140 endemic species, including 6 problematic ones. South-west Asia as a whole is an area of considerable diversity and endemism of the Umbelliferae.
Membrane attack and therapy in autoimmune disease: modulating pathology whilst retaining physiology

I have created novel anti-complement reagents designed to deliver effective therapy locally, or where inhibition is long-term, to target only the terminal stages of complement. These agents have exciting potential to effectively treat complement-mediated diseases and to retain other crucial biological functions of complement such as opsonisation and immune complex solubilisation.
Immune response of chicken to an experimental sonicated coccidia oocyst vaccine

A total of 120 one-day old broiler chicks (Ross breed) were used to evaluate the humoral immune response of vaccine-I (supernatent from sonicated sporulated oocyst), vaccine-II (sediment from sonicated sporulated oocysts) and vaccine-III (un-sonicated sporulated oocyst) against coccidiosis in chicks was determined by indirect haemagglutination (IHA) test. IHA antibody titre was significantly higher (p<0. 05) in chicks vaccinated with vaccine-I as compare to vaccine-II and vaccine-III. The IHA antibody titre of chicks vaccinated with vaccine-I ranged from 1:7 to 1:7012, 1:16 to 1:410 for vaccine II and 1:2 to 1:64 for vaccine III. Vaccine I gave 100 percent protection and oocysts appeared in the faeces (100-200 oocysts per grams) on day 11 post challenge which gradually number of oocysts increased, 650 to 900 oocysts per grams on day 17 and 200-400 on day 21 post challenge. Vaccine-II gave 62 percent protection and oocyst appeared in the faeces (300,000-400,000 oocysts) on day9 post challenge which gradually increased (800,000-900,000 oocysts) on day 17 and 100,000-200,000 on day 21post challenge. Vaccine III gave 33 percent protection and oocyst appeared in the faeces (800,000-900,000) on day 8 post challenge which gradually increased (100,000-1,250,000 per grams) on day 17 and 840,000 - 900,000 on day 21 post challenge. In control group, characteristic bloody diarrhoea was observed in all the chicks and oocysts appeared in the faeces (1,000,000-1,250,000 per grams) on day 6 post challenge of faeces which gradually increased (1,400,000-1,750,000 per grams) on day 17 post challenge. the overall findings of this study indicate that the humoral and challenge response of the Vaccine I indicated a strong protection as immune chicks contained high level of antibodies that resisted heavy dose of challenge and gave 100 percent protection.
Investigations on mercury sensitivity and molecular determinants of selectivity in two plant aquaporins.

Aquaporins (AQPs) are members of major intrinsic proteins and form water conducting channels in the biological membranes. These may also transport small solutes as well as gases. The latter are, however, considered to be transported through a separate tetrameric pore. Not much is known about the structure of plant AQPs, particularly in case of TIP sub-family, no structural data is so far available. In the present study, detailed point mutational as well as transmembrane domain swapping analyses were performed to understand the molecular determinants of selectivity in AQPs. The mutational analysis involved substitutions of the native Cys residues in TaTIP2;2 and introduction of an already known Hg-sensitive site belonging to another TIP isoform (gamma-TIP). The results revealed that the presence of a Cys at a particular site in TM3 of the plant TIPs would render them Hg-sensitive. This lead to proposing a consensus region of metal sensitivity in plant AQPs (similar to the one in mammalian AQPs) for accommodating a Hg-sensitive Cys. A significant part of the study involved identification of molecular signatures of selectivity located both inside and outside the selectivity regions (ar/R region and NPA motif) of AQPs. The sequence alignment including predominantly water conducting AQPs in comparison to the ammonia conducting ones suggested a couple of positions with the residues distinguishable between the two AQP sub-families. The amino acid substitutions at the corresponding positions of TaTIP2;2 and NtPIP2 couldn’t turn the PIP into an ammonia-conducting channel however, a drastic effect of the said mutations on water permeability of PIP (and not of TIP) was observed suggesting their role in the water transport function of the PIPs sub-family. As TIP mutants retained their ammonia transport function similar to the wild type, the varying effects of the given residues may be attributed to the difference in structure between TIPs and PIPs besides pointing towards the presence of a central pore in AQPs. As regards the mutations inside the selectivity regions, none of the mutants was functional for water and ammonia transport. Same was the case with a number of chimeric proteins containing different transmembrane domains swapped between TIP and PIP. However, the leakage of protons could be demonstrated in some of these AQP variants. For future studies, the joint mutations combining the molecular signatures suggested in the present study with those located inside the selectivity regions may help to further understand the molecular mechanism of selectivity.
GENOME-WIDE SELECTION SIGNATURES IN PINZGAU CATTLE

The aim of this study was to identify the evidence of recent selection based on estimation of the integrated Haplotype Score (iHS), population differentiation index (FST) and characterize affected regions near QTL associated with traits under strong selection in Pinzgau cattle. In total 21 Austrian and 19 Slovak purebreed bulls genotyped with Illumina bovineHD and bovineSNP50 BeadChip were used to identify genomic regions under selection. Only autosomal loci with call rate higher than 90%, minor allele frequency higher than 0.01 and Hardy-Weinberg equlibrium limit of 0.001 were included in the subsequent analyses of selection sweeps presence. The final dataset was consisted from 30538 SNPs with 81.86 kb average adjacent SNPs spacing. The iHS score were averaged into non-overlapping 500 kb segments across the genome. The FST values were also plotted against genome position based on sliding windows approach and averaged over 8 consecutive SNPs. Based on integrated Haplotype Score evaluation only 7 regions with iHS score higher than 1.7 was found. The average iHS score observed for each adjacent syntenic regions indicated slight effect of recent selection in analysed group of Pinzgau bulls. The level of genetic differentiation between Austrian and Slovak bulls estimated based on FST index was low. Only 24% of FST values calculated for each SNP was greather than 0.01. By using sliding windows approach was found that 5% of analysed windows had higher value than 0.01. Our results indicated use of similar selection scheme in breeding programs of Slovak and Austrian Pinzgau bulls. The evidence for genome-wide association between signatures of selection and regions affecting complex traits such as milk production was insignificant, because the loci in segments identified as affected by selection were very distant from each other. Identification of genomic regions that may be under pressure of selection for phenotypic traits to better understanding of the relationship between genotype and phenotype is one of the challenges for livestock genetics.