Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete mitochondrial genome of a parasitic flatworm Senga ophiocephalina (Cestoda: Bothriocephalidae)

Abstract Mitochondrial DNA of nematodes undergoes frequent rearrangements, so it is a very good model for studying the mitochondrial genome evolution. The complete mitochondrial genome of a parasitic nematode Senga ophiocephalina was sequenced and annotated. The 13,816 bp-long genome contained 12 protein-coding genes (atp8 gene was missing), two ribosomal RNAs, 22 transfer RNAs, and a 391 bp non-coding region. Phylogenetic analysis showed that S. ophiocephalina forms a monophyletic cluster with the remaining two Bothriocephalidae species.
Identification of Quantitative Trait Loci for Vigorous Root Development under Water-Deficiency Conditions in Rice

Seedling vigor in drought stress conditions is an important characteristic of the dry direct-seeded rice system. The drought stress in the seedling stage disrupts seed germination and delays the establishment of seedlings. However, little is known about the genetic mechanism of seedling vigor in drought conditions. The identification of quantitative trait loci (QTL) was conducted using 162 recombinant inbred lines (RILs) derived from a cross between two rice varieties — a Tongil-type Milyang23 and a temperate japonica Tong88-7. The seedling vigor of these RILs was characterized by measuring 10 morphological traits of the seedlings grown under drought conditions. The Tong88-7 seedlings showed significantly higher values than the Milyang23 seedlings for all traits. The genotyping-by-sequencing method was used to construct a map of 6140 single nucleotide polymorphisms. Six main-effect QTLs (M-QTLs) associated with seedling vigor traits under drought stress were identified on chromosomes 9 and 11. In particular, five out of these six QTLs were located on chromosome 11, explaining the phenotypic variances of 4.3% through 10.1%. In addition, 21 epistatic QTLs (E-QTLs) were detected, and the 27 loci involved in this interaction were distributed on 11 chromosomes. Both M-QTLs and E-QTLs detected in this study would be useful in breeding programs to develop elite rice varieties especially adapted to dry direct-seeded rice system.
Two-stage adaptation of inhibition mediates predictive sensitization in the retina

A critical function of the nervous system is the prediction of future sensory input. One such predictive computation is retinal sensitization, a form of short-term plasticity seen in multiple species that elevates local sensitivity following strong local stimulation. Here we perform a causal circuit analysis of retinal sensitization using simultaneous intracellular and multielectrode recording in the salamander. We show, using direct current injection into inhibitory sustained amacrine cells that a decrease in amacrine transmission is necessary, sufficient and occurs at the right time and manner to cause sensitization in ganglion cells. Because of neural dynamics and nonlinear pathways, a computational model is essential to explain how a change in steady inhibitory transmission causes sensitization. Whereas adaptation of excitation removes an expected result in order to transmit novelty, adaptation of inhibition provides a general mechanism to enhance the sensitivity to the sensory feature conveyed by an inhibitory pathway, creating a prediction of future input.
Disentangling the Peltigera polydactylon Species Complex by Recognizing Two New Taxa, P. polydactylon subsp. udeghe and P. seneca

Abstract: Magain, N. , Sérusiaux, E. , Zhurbenko, M. P., Lutzoni, F. & Miadlikowska, J. 2016. Disentangling the Peltigera polydactylon species complex by recognizing two new taxa, P. polydactylon subsp. udeghe and P. seneca. — Herzogia 29: 514–528. A new species, Peltigera seneca, and two subspecies within P. polydactylon (s.str.), P. polydactylon subsp. udeghe and P. polydactylon subsp. polydactylon, were segregated from a broadly defined P. polydactylon s.lat. , based mostly on molecular data and distinct geographical ranges. Peltigera polydactylon s.str. and P. seneca form well-supported monophyletic lineages that share a most recent common ancestor and were recognized as two distinct species by multiple species delimitation and validation methods. Peltigera polydactylon s. str. has a broad intercontinental distribution whereas the new species P. seneca is restricted to eastern North America where it seems to be rare. Peltigera polydactylon subsp. udeghe and P. polydactylon subsp. polydactylon, were defined to accommodate two monophyletic and strongly supported clades separated geographically (North America, eastern Northern Asia and Australasia versus Europe, Middle East and central Northern Asia, respectively). Despite the low genetic distance, especially for the ITS, between these two subspecies, they are well segregated genetically throughout their allopatric ranges. However, there seems to be an intermediary pattern of variation in the geographical area where both taxa are likely to co-occur (e.g., central and eastern Northern Asia). Phenotypic traits have limited value in distinguishing these three taxa. They are chemically (secondary metabolites) similar and share the same Nostoc (cyanobiont) phylogroup. Nevertheless, there are helpful phenotypic trends in addition to their diagnostic genotypes.
INCIDENCE OF COFFEE WHITE STEM BORER, Xylotrechus ‘quadripes (Chevr.) (COLEOPTERA : CERAMBYCIDAE) ON TEAK, Tectona grandis L.

The coffee white stem borer, Xylotrechur quadripes (Chevr.) is a serious pest of arabica coffee, Cojffea arabica L. in India. The pest has been reported on arabica coffee in India as early as 1867 (Subramaniam, 1934). Though, coffee is the principal host of X. quadripes, the pest is known to attack occasionally Olea dioica L. (Subramaniam, 1934), robusta coffee, Coﬁea cartephora Pierre ex Froehner (Beeson and Bhatia, 1939), tree coffee, Coﬂee liberica Bull ex Hiren (Duport, 1915) and teak, Tectona grandis L. (Mayne, 1930) in India. The borer incidence on teak is of concern as it is widely grown in coffee plantations and is likely to form a reservoir for pest infestation.
A new method for identification of pre-microRNAs based on hybrid features

<strong>Background:</strong>The identification of pre-microRNAs (precursor microRNAs) helps us<br/>to understand the regulatory mechanism of biological processes. <br/>Currently, machine learning is the most popular method for<br/>pre-microRNA identification. However, most methods mainly focus on<br/>secondary structure information of pre-microRNA, while ignoring<br/>sequence-order information and sequence evolution information. <strong>Results:</strong><br/>In this work, we use three different methods to<br/>extract features of the pre-microRNAs at different levels. We first<br/>extract features from PSI-BLAST profiles and Hilbert-Huang<br/>transform, which contain rich sequence evolution information and<br/>sequence-order information respectively. We then get properties of<br/>small molecular networks of pre-microRNAs, which contain refined<br/>secondary structure information. We extract 591 features in total. <br/>After extraction, we use support vector machine (SVM) as our<br/>classifier, and use the maximum relevance and minimum redundancy<br/>(mRMR) method for feature selection. Finally, we construct a new<br/>predictor <em>MicroRNA-NHPred</em> by using the optimal feature set. <br/>The performance of <em>MicroRNA-NHPred</em> is quite promising<br/>compared to other popular miRNA predictors. It achieves an accuracy<br/>of up to 94.83\%. <strong>Conclusions:</strong><br/>The higher prediction accuracy achieved by our proposed method is<br/>attributed to the design of a comprehensive feature set on the<br/>sequence and secondary structure, which are capable of<br/>characterizing the sequence evolution information and sequence-order<br/>information, and global and local information of pre-microRNAs<br/>secondary structure. Therefore, it is a valuable method to<br/>pre-microRNAs identification.
Molecular Mechanisms of Group B Streptococcus Urinary Tract Infection and Adaptability to Growth in Human Urine

Bacteriuria, or the presence of bacteria in urine, is associated with both asymptomatic, as well as symptomatic urinary tract infection (UTI) and underpins much of the dynamic of microbial colonization of the urinary tract. The prevalence of bacteriuria in dissimilar patient groups such as healthy adults, institutionalized elderly, pregnant women, and immune-compromised patients varies widely. In addition, assessing the importance of ‘significant bacteriuria’ in infected individuals represents a diagnostic challenge, partly due to various causal microbes, and requires careful consideration of the distinct etiologies of bacteriuria in different populations and circumstances. Recent molecular discoveries have revealed how some bacterial traits can enable organisms to grow in human urine, which, as a fitness adaptation, is likely to influence the progression of bacteriuria in some individuals. This study was designed as a comprehensive analysis of asymptomatic bacteriuria (ABU) causal organisms in dissimilar populations, and an in-depth microbiological analysis of the mechanisms used by one such causal organism, Streptococcus agalactiae. This organism causes UTI including ABU; however, growth of S. agalactiae in human urine has not been reported. In the first part of this study, we evaluate the prevalence and etiology of bacteruria, and discuss recent advances in the molecular detection of bacteriuria from a diagnostic viewpoint.
Inbreeding in an endangered killer whale population

There are genetic risks associated with small population sizes, including loss of genetic diversity and inbreeding depression. The southern resident killer whale Orcinus orca population is a group of ~80 whales listed as ‘endangered’ under the U.S. Endangered Species Act. Recovery efforts are focused on increasing prey and reducing impacts from environmental disturbance, but the population's small size and insularity suggest that inbreeding depression could also be important. We analyzed genotypes at 68–94 nuclear loci from 105 individuals to refine a population pedigree to evaluate inbreeding and the relationship between multi‐locus heterozygosity and fitness. Our results expand upon an earlier study and shed new light on both inbreeding within this population and the mating patterns of killer whales. We found that only two adult males sired 52% of the sampled progeny born since 1990. Confirming earlier results, we found male reproductive success increased with age. Based on the pedigree, four sampled offspring were the result of inbred mating – two between a parent and offspring, one between paternal half‐siblings, and one between uncle and half‐niece. There is no evidence to date that the survival or fecundity of these individuals is lower than normal. There was some evidence for inbreeding depression in the form of a weakly supported relationship between multi‐locus heterozygosity and annual survival probability, but the power of our data to quantify this effect was low. We found no evidence of inbreeding avoidance in the population, but a late age of breeding success for males may indirectly limit the frequency of parent/offspring mating. The effective number of breeders in the population is currently ~26, and was estimated to have ranged from 12–53 over the past 40 years. The population that produced the oldest (pre‐1970) sampled individuals was estimated to have 24 effective breeders. Overall, our results indicate that inbreeding is likely common in the population, but the fitness effects continue to be uncertain.
Vegetation structure, species life span, and exotic status elucidate plant succession in a limestone quarry reclamation

An understanding of the processes involved in plant succession is pivotal in achieving an effective site restoration. In a former limestone quarry (northeastern Italy), we explored the effects of a technical reclamation on the plant community using changes in cover of vegetation layers and two sensitive plant traits (i.e. exotic status and life span), with a chronosequence approach. Four reclaimed areas of different ages (from 8 to 35 years old) and natural vegetation in the surroundings were investigated with seven permanent plots each, for a total of 35. Changes in vegetation layers and species richness of both exotic status and life span were analyzed by generalized linear (mixed) models. Relations with plant community assembly were also considered, using a multivariate approach. Both vegetation layers and plant traits were affected by the age of reclaimed areas, evidencing the main changes in plant succession. Annual and exotic species decreased toward the mature stages of reclamation and target vegetation, whereas overall plant diversity (species richness) was stable. Our findings show that both vegetation layer changes and plant traits can be used to assess the degree to which reclamation efforts produce results that approach the restoration of a natural vegetation reference. Implementation of management practices aimed at favoring native perennial species (e.g. appropriate seed mixtures, mowing, tree, and shrub planting) could limit weed‐control efforts, representing a reasonable trade‐off between biodiversity promotion and invasive plant control.
In vitro digestion models for dietary phenolic compounds

The aim of this work was to develop in vitro digestion models for mimicking the physiological conditions of upper intestine and microbial conversions in the colon. The main emphasis was on the microbial metabolism of plant phenolic compounds: pure quercetin derivatives, pure anthocyanins and lignans from rye bran and flaxseed. When cereal samples are introduced to an in vitro colon model a removal of digestible components is needed. An enzymatic in vitro digestion model was developed for maximal starch removal from cereal samples. Pepsin, pancreatin and bile concentrations were optimized using an experimental design. Surprisingly, pepsin and bile also affected the extent of starch hydrolysis in synergy with pancreatin. 511 % of the original amount of starch remained in the residues of cereal products. Proteins were also partly hydrolysed. The in vitro enzymatic digestion model was used for the pretreatment of rye bran and flaxseed samples. An anaerobic in vitro colon model, conventionally used for the fermentation of non-digestible carbohydrates, was developed further for studying pure phenolic compounds. Human faecal microbiota from several healthy donors was used in the preparation of an inoculum. A low inoculum concentration was used for decreasing the metabolite concentration from the faecal background in the studies concerning pure flavonoids. A dense faecal suspension was suitable for the conversion of rye bran and flaxseed lignans to enterolactone when the plant matrix was present. Flavonoids were deconjugated and degraded to phenolic acids by faecal microbiota. Specific activities of the deconjugative enzymes from the
Influence of fire and mechanical sagebrush reduction treatments on restoration seedings in Utah, United States

Overabundance of woody plants in semiarid ecosystems can degrade understory herbaceous vegetation and often requires shrub reduction and seeding to recover ecosystem services. We used meta‐analysis techniques to assess the effects of fire and mechanical shrub reduction over two post‐treatment timeframes (1–4 and 5–10 years) on changes in cover and frequency of 15 seeded species at 63 restoration sites with high potential for recovery. Compared to mechanical treatments, fire resulted in greater increases in seeded species. Native shrubs did not increase, and forbs generally declined over time; however, large increases in perennial grasses were observed, suggesting that seeding efforts contributed to enhanced understory herbaceous conditions. We found greater increases in a few non‐native species than native species across all treatments, suggesting the possibility that interference among seeded species may have influenced results of this regional assessment. Differences among treatments and species were likely driven by seedbed conditions, which should be carefully considered in restoration planning. Site characteristics also dictated seeded species responses: while forbs showed greater increases in cover over the long term at higher elevation sites considered to be more resilient to disturbance, surprisingly, shrubs and grasses had greater increases in cover and frequency at lower elevation sites where resilience is typically much lower. Further research is needed to understand the causes of forb mortality over time, and to decipher how greater increases of non‐native relative to native seeded species will influence species diversity and successional trajectories of restoration sites.
Exploring mechanisms of long range gene regulation at the Pax6 locus

PAX6 belongs to a highly conserved protein family with key functions in patterning the embryo. The PAX6 gene plays a crucial role in eye development and is essential for normal development of the brain, olfactory system and endocrine pancreas. Pax6 expression is subject to strict spatial, temporal and quantitative regulation and complex control mechanisms are utilised to achieve this. The boundaries of this complex locus have been defined through human aniridia-associated breakpoints and mouse studies. A locus-wide DNase I hypersensitive site (HSS) analysis was carried out to identify active (or "open") regulatory elements in cell lines of different origin that do (MV+ and N2A) and do not (RAG) express Pax6. Many HSSs coincided with previously identified regulatory sequences, while others mapped to genomic elements such as repetitive DNA elements and CpG islands. Some HSSs appear to be cell line specific, while others were found in all three. Some of the regulatory elements identified are separated by over 150 kb on the linear DNA molecule. How cA-elements located at such large distances from the promoter(s) of the gene can control transcription is a major problem to address. Active cA-elements at a small number of other loci have been shown to cluster within the nucleus in cells expressing the regulated gene. This clustering is proposed to form a transcription factory, providing a high density of factors for interaction with the promoter(s). To explore such interactions at the Pax6 locus, chromosome conformation capture (3C) was used to determine the relative cross-linking frequencies of a number of anchor points with a series of DNA fragments spanning the locus, in each of the three cell lines described above. Surprisingly, broadly similar levels of association were seen in each cell line, with subtle differences that did not exactly correlate to HSS activity. Findings were mirrored in Pard-expressing forebrain (E14.5) and cortex cells (E17.5) and Pax(5-negative embryonic liver revealing that these associations are not confined to immortalised cell lines. These results suggest a model whereby some regulatory elements do appear to be in close
Can Microgravity Alter the Ability of the Brain to Self-Repair?

The effects of spaceflight on the human body are largely unknown. Research suggests that spaceflight results in a decline of cognitive ability, although the reasons behind it are not known. The purpose of our study was to test the hypothesis that simulated microgravity would impair the function of neural stem cells. Neural stem cells function to produce the different cell types in the brain, in addition to more stem cells. To test our hypothesis, we isolated and cultured cells in vitro from embryonic chicken brains in neurosphere assays with growth factors. Neurosphere assays test for stem cells via their function –the ability to produce more stem cells (to self-renew) and the different cell types in the brain. We assessed the number of neurospheres and, using antibodies specific to each cell type, their ability to produce the three main types of neural cells in the brain, neurons, astrocytes and oligodendrocytes. Confocal laser-scanning microscopy was used to capture images of the fluorescent labels attached to each cell type. Initial experiments were performed under normal gravity, whereas future experiments will be under simulated microgravity. We hope to discover whether or not simulated microgravity has an effect on the function of neural stem cells. Faculty Mentor: Barbara Murdoch
A new and rare species of Nymphoides (Menyanthaceae) from the North West of Western Australia

Davis, R.W. , Hammer, T.A. & Thiele, K.R. A new and rare species of Nymphoides (Menyanthaceae) from the North West of Western Australia. Nuytsia 27: 245–252 (2016). Nymphoides walshiae R.W. Davis & K.R. Thiele, a new and rare species of Nymphoides Ség. , is described. This new species is geographically disjunct from other Nymphoides species, occurring in a small area of arid Western Australia near the Cape Range. A molecular phylogenetic analysis based on ITS sequences suggests that it occupies a phylogenetically isolated position sister to the largest clade in the genus. It lacks some of the more common features seen in the genus Nymphoides. A scanning electron microscope image displaying the seed surface and outline is provided.
Haematopinus Infestations and Mycoplasma Infections of Water Buffalo (Bubalus bubalis) Herds in National Parks of Hungary

The biology, epidemiology and pathology of sucking louse infestation and Mycoplasma infection of water buffalo ( Bubalus bubalis ) herds in Hungarian national parks were studied between 19 December 2011 and 4 May 2012. A total of 333 water buffaloes were examined in buffalo stocks of the Balaton Uplands, FertA‘-HansAig and KiskunsAig National Parks. The objective was to determine the prevalence and rate of sucking louse infestation and mycoplasma infection among water buffaloes. Always an area of identical size (2 cm 2 ) was examined on the right or left side of the middle part of the animalsâ€™ neck. A total of 3106 eggs, 10 nymphs and 105 adults of the sucking louse Haematopinus tuberculatus were identified with the help of a Conrad USB microscopic camera and a Wild-Leitz-Leica M420 photomacroscope. The data were evaluated using the Quantitative Parasitology software QP 3.0. The prevalence of mycoplasmas was determined in 20 randomly selected buffaloes of two national parks with the help of sterile nasal and vaginal transport swabs (Sarstedt). All of the 10 nasal swabs collected from buffaloes in the Balaton Uplands National Park contained Mycoplasma bovirhinis and three swab samples yielded M. bovis as well. Mycoplasma bovirhinis was cultured from 8 out of 10 swabs taken from the vagina, and three vaginal samples also yielded M. bovis . Similar results were obtained by testing samples collected from buffaloes in the KiskunsAig National Park (MA³rahalom). All ten nasal swab samples yielded M. bovirhinis . From two samples a mixture of M. bovirhinis and M. bovis was cultured. Nine out of the 10 vaginal swabs yielded M. bovirhinis while two showed a combined infection by M. bovis and M. bovirhinis .