Miracle-dz/UniFAR-FTUs huggingface dataset:
Land-use change on Mount Gede, Indonesia, reduced native earthworm populations and diversity

Abstract. The conversion of natural forest to agroforestry plantations and annual cropping systems alters the soil habitat and food resources for biota, including earthworms. Native earthworm species may disappear whereas exotic species with greater tolerance of disturbance and less niche specialisation may thrive. The objective of the study was to compare the earthworm diversity in managed forest and agroforestry systems, which were cultivated for mixed plantation and annual crop production on Mount Gede, Indonesia. All the habitats in the study area were impacted by humans. The forest habitat was a managed forest, with a permanent tree cover, whereas mixed plantation had a partial shrub cover. Meanwhile, homogenous plantation was cultivated with annual crops. Among 3787 individuals collected during July–October 2012, five Oriental earthworm species were identified in the soil communities of Mount Gede: Drawida nepalensis, Notoscolex javanica, Pheretima pura-group, Polypheretima moelleri, and Polypheretima sempolensis. Also, 18 species were found that are reported to be non-Oriental in origin. Anthropogenic disturbance of forests on Mount Gede, due to conversion into plantations, alters the earthworm environment by increasing soil water content, temperature and total phosphorous content, while decreasing organic carbon. N. javanica was the only native species to survive this deforestation, while the exotic Ocnerodrilus occidentalis and Pontoscolex corethrurus thrived, becoming the eudominant species. From the forest area to the mixed and homogenous plantations, the predicted decreasing diversity is evidenced by the lowering trend of Shannon’s diversity index. In conclusion, the land-use change into mixed plantations and annual croplands has reduced earthworm diversity in this region of Mount Gede, Indonesia.
Classi¢cation and phylogeny of hydrogenases 1

Hydrogenases (H2ases) catalyze the reversible oxidation of molecular hydrogen and play a central role in microbial energy metabolism. Most of these enzymes are found in Archaea and Bacteria, but a few are present in Eucarya as well. They can be distributed into three classes: the [Fe]-H2ases, the [NiFe]-H2ases, and the metal-free H2ases. The vast majority of known H2ases belong to the first two classes, and over 100 of these enzymes have been characterized genetically and/or biochemically. Compelling evidence from sequences and structures indicates that the [NiFe]- and [Fe]-H2ases are phylogenetically distinct classes of proteins. The catalytic core of the [NiFe]-H2ases is a heterodimeric protein, although additional subunits are present in many of these enzymes. Functional classes of [NiFe]-H2ases have been defined, and they are consistent with categories defined by sequence similarity of the catalytic subunits. The catalytic core of the [Fe]-H2ases is a ca. 350-residue domain that accommodates the active site (H-cluster). A few monomeric [Fe]-H2ases are barely larger than the H-cluster domain. Many others are monomeric as well, but possess additional domains that contain redox centers, mostly iron^sulfur. Some [Fe]H2ases are oligomeric. The modular structure of H2ases is strikingly illustrated in recently unveiled sequences and structures. It is also remarkable that most of the accessory domains and subunits of H2ases have counterparts in other redox complexes, in particular NADHubiquinone oxidoreductase (Complex I) of respiratory chains. Microbial genome sequences are bringing forth a significant body of additional H2ase sequence data and contribute to the understanding of H2ase distribution and evolution. Altogether, the available data suggest that [Fe]-H2ases are restricted to Bacteria and Eucarya, while [NiFe]-H2ases, with one possible exception, seem to be present only in Archaea and Bacteria. H2ase processing and maturation involve the products of several genes which have been identified and are currently being characterized in the case of the [NiFe]-H2ases. In contrast, near to nothing is known regarding the maturation of the [Fe]-H2ases. Inspection of the currently available genome sequences suggests that the [NiFe]-H2ase maturation proteins have no similar counterparts in the genomes of organisms possessing [Fe]-H2ases only. This observation, if confirmed, would be consistent with the phylogenetic distinctiveness of the two classes of H2ases. Sequence alignments of catalytic subunits of H2ases have been implemented to construct phylogenetic trees that were found to be consistent, in the main, with trees derived from other data. On the basis of the comparisons performed and discussed here, proposals are made to simplify and rationalize the nomenclature of H2ase-encoding genes. fl 2001 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
Identifying Tissue Specific Distal Regulatory Sequences in the Mouse Genome

Epigenetic modifications, transcription factor (TF) availability and chromatin conformation influence how a genome is interpreted by the transcriptional machinery responsible for gene expression. Enhancers buried in non-coding regions are associated with significant differences in histone marks between different cell types. In contrast, gene promoters show more uniform modifications across cell types. In this report, enhancer identification is first carried out using an enhancer associated feature in mouse erythroid cells. Taking advantage of public domain ChIP-Seq data sets in mouse embryonic stem cells, an integrative model is then used to assess features in enhancer prediction, and subsequently locate enhancers. Significant associations with multiple TF bound loci, higher expression in the closest genes, and active enhancer marks support functionality and tissue-specificity of these enhancers. Motif enrichment analysis further determines known and novel TFs regulating the target cell type. Furthermore, the features identified can facilitate more accurate enhancer prediction in
07. Acoustic communication in a Neotropical frog ( Dendropsophus minutus ): vocal repertoire, variability and individual discrimination

Correspondence: Alessandro R. Morais, Programa de Pós-Graduação em Ecologia & Evolução, Universidade Federal de Goiás, Caixa Postal 131, Goiânia, Goiás, Brazil; E-mail: alessandrogyn@hotmail.com Acoustic signals are the most important communication mechanism for many anuran species. However, acoustic parameters can be influenced by several factors (e.g., body size, air temperature and social context). In the present study, we investigated the influence of the air temperature, morphological characteristics and distance between calling males on acoustic parameters of Dendropsophus minutus. In addition, we studied the entropy values of calls, acoustic variability (both within and among males) and the potential for individual discrimination. The observations were carried out between January 2009 and April 2011, in Piracanjuba, Goiás, central Brazil. Males of D. minutus emitted single and compound calls, composed by notes A, B and C. We observed that vocalizations may be influenced by snout-vent length, body mass, air temperature and distance between calling males (P<0.05 in all cases). Dominant frequency was the only variable classified as a static property. There was higher variability among males than within males in all parameters measured. Individual males of D. minutus may be discriminated by their vocalizations, with dominant frequency being the main acoustic variable used in individual discrimination. We conclude that the high variation in D. minutus calls might be important during mate choice process.
Glucose transporters in pearl gentian grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂): molecular cloning, characterization, tissue distribution and their expressions in response to dietary carbohydrate level.

The glucose transporters (GLUTs) play vital role in mediating the glucose uptake process, the movement of glucose across plasma membranes. In this study, three GLUTs, GLUT1, GLUT2 and GLUT4 were cloned and characterized form pearl gentian grouper, a hybrid grouper, and their expressions in response to dietary carbohydrate level (8.02%, 11.89% and 16.08%) were investigated after feeding. The full-length cDNA of GLUT1, GLUT2 and GLUT4 were 2,104, 3,759 and 2,815 bp, respectively, encoding a putative protein of 491, 508 and 505 amino acids respectively. The results of sequence and phylogenetic analysis revealed that grouper GLUTs were highly conserved and clustered together with their corresponding teleost orthologues, rather than mammals. In addition, GLUT1 was ubiquitously expressed in all detected tissues with relative high expressions in heart and brain. GLUT2 is relatively abundant in some certain tissues that release glucose, such as liver and intestine, and GLUT4 was expressed primarily in muscle and eye. The elevated dietary carbohydrate level had no significant difference on the expression of GLUT1 in grouper liver. The expression of GLUT2 in grouper liver was significantly up-regulated with the increasing dietary carbohydrate from 8.02% to 11.89%, and therefore down-regulated significantly. Meanwhile, the expression of GLUT4 in grouper muscle increased significantly with increasing dietary carbohydrate. Results of this study indicate that the up-regulation of GLUTs in fish contribute to maintain glucose equilibrium to some extent when fish were fed with high carbohydrate diets.
Histological Effect of Ursolic Acid, Hyperinsulinemia and Vitamin B Complex on Sciatic Nerve Repair and Lipid Profile of Alloxan induced Diabetic Rabbits

تهدف هذه الدراسة إلى تقييم تأثير حامض الأورسوليك، فرط الأنسولين وفيتامين ب المركب على إصلاح العصب الوركي في ذكور الأرانب المصابة بمرض السكري، وتحديد آثارها على الدهون في الدم وكشف آثارها على التركيب النسيجي للعصب الوركي. وأظهرت نتائج هذه الدراسة أن السكري المستحدث بالألوكسان تسبب في زيادة نسبة الكوليسترول والدهون الثلاثية في الدم في حين العلاج باستخدام حامض الأورسوليك المستخلص والقياسي، فرط الانسولين وفيتامين ب المركب سبب انخفاضا كبيرا في نسبة الكولسترول والدهون الثلاثية في الدم (p<0.05). هناك انخفاض ملحوظ في البروتين الدهني عالي الكثافة (HDL) وزيادة كبيرة في البروتين الدهني منخفض الكثافة (LDL) في الدم وجد في مجموعات السكري وفرط الانسولين، في حين أن هناك زيادة كبيرة في (HDL) في جميع مجاميع العلاج باستثناء مجموعة فرط الانسولين. من ناحية أخرى، هناك انخفاض ملحوظ في (LDL)، خاصة في مجموعة حامض الأورسوليك المستخلص (p<0.05). لقد بينت المقاطع النسيجية للعصب الوركي انحلال الألياف العصبية يبدو كمناطق تورم غير واضحة وتحلل دهني للألياف العصبية بسبب عملية سحق العصب. بعد العلاج هناك العديد من التغييرات المختلفة التي دلت على وجود تحسن في العصب الوركي اختلفت هذه التغيرات وفقا لنوع العلاج.
Long-term effects of beach nourishment on intertidal invertebrates

Author(s): Wooldridge, Tyler Brock | Abstract: Although beach nourishment is an increasingly popular means to remediate coastal erosion, no consensus exists regarding how long nourishment affects sandy beach intertidal invertebrates, key components of sandy beach ecosystems. We monitored the intertidal invertebrate community for fifteen months following a nourishment project at eight beaches across San Diego County. Each beach was split into nourished and control sections. Nearly all taxa showed major declines in abundance immediately following nourishment. Populations of Talitrid amphipods and the bean clam Donax gouldii recovered within one year, sooner than in previous studies. Populations of the mole crab Emerita analoga bloomed at four months after nourishment, and were more numerous on nourished portions of beaches at that time. Mole crab populations subsequently declined and no longer differed by treatment. The polychaete community, composed of Scolelepis spp. and several other numerically important taxa, showed a strong nourishment-induced reduction in abundance that persisted through the end of the study. The large negative effect of nourishment on polychaetes, coupled with their overall importance to the invertebrate community, resulted in a more than twofold reduction in overall invertebrate abundance on nourished beaches at 15 months. Such reductions may have far reaching consequences for sandy beach ecosystems, as community declines can reduce prey availability for shorebirds and fish. As this and other recent studies have revealed longer times for the recovery of intertidal invertebrates than previously observed, more cautious estimates regarding the magnitude and duration of impacts of beach nourishment should be applied to management practices
Role of multi-site phosphorylation in regulation of E(spl) M8 activity during Drosophila neurogenesis

Role of multi-site phosphorylation in regulation of E(spl) M8 activity during Drosophila neurogenesis Mohna Bandyopadhyay Notch signaling is an evolutionarily conserved pathway that regulates cell-fate determination at various stages of development in invertebrate and vertebrate species. The Notch pathway mediates juxtacrine signaling through a process termed as lateral inhibition by which two equipotent cells adopt distinct cell fates. The functions of Notch have been exceptionally well analyzed during neurogenesis in Drosophila, particularly during eye and mechanosensory bristle morphogenesis. At the onset of neurogenesis, proneural bHLH activators encoded by atonal (ato) or the achaete-scute complex (ASC) is expressed in groups of cells, called proneural clusters (PNCs) in the eye and the bristle tissue respectively. From each PNC, however, only a single cell becomes the neural progenitor, the sensory organ precursor (SOP). This selection is mediated through E(spl) repressors, a group of evolutionary conserved bHLH repressors and the terminal effectors of the Notch pathway. Accumulating evidence suggest that repression of Ato/ASC by E(spl) occurs in a phosphorylation dependent manner. Protein kinase CK2 phosphorylates E(spl)-M8, which then undergoes a conformational change and antagonizes the proneural proteins. The work described in this dissertation aims to provide a more detailed understanding of the mechanism of neural repression by M8. The work described in Chapter 2 provides in vivo evidence that multi-site phosphorylation of the C-terminal domain (CtD) of M8 may be involved in regulation of repressor activity. Using phospho-mimetic variants of M8 we have shown that both CK2 and MAPK motif in the CtD may be modulated for the protein to exhibit neural repression. Multisite phosphorylation may act as a ‘switch’ controlling the activity and onset of repression by M8 during neurogenesis. The studies in Chapter 3 demonstrate a direct role of P-domain, a conserved phosphorylation domain of CtD, in autoinhibition model of M8. The deletion variant studies provide strong evidence that the P-domain provides critical autoinhibitory contact with HLH and/or Orange domain to regulate repression of Ato/ASC. This study provides a fundamental reinterpretation of the mechanism by which truncated protein, M8* encoded by m8 allele E(spl)D, that lacks the autoinhibitory domain, elicits precocious Ato antagonism thus interfering with first phase of Notch signaling and perturbing eye development. Our studies also implicate P-domain as a target of Slmb, a subunit of E3 ubiquitin ligase that may give rise to ‘phosphodegron’ necessary for proteasomal degradation and rapid clearance of M8. Together, the studies described in this dissertation provide a mechanism of M8 regulation by posttranslational regulation to elicit the effects of inhibitory Notch signaling during lateral inhibition.
THE MOLECULAR AND BEHAVIORAL CONSEQUENCES OF ABNORMAL NORADRENERGIC NEUROTRANSMISSION IN THE HYPERACTIVE SNAP-25 DEFICIENT MOUSE MUTANT COLOBOMA

Attention Deficit Hyperactivity Disorder (ADHD) is the most common pediatric neuropsychiatric disorder. The disorder has a genetic component and affects nearly 2 million American children. An imbalance between dopaminergic and noradrenergic systems has been implicated in ADHD and Tourette's syndrome, a common comorbid condition. Indeed, many drugs used to treat hyperactivity act on both dopaminergic and noradrenergic systems. However, the mechanism(s) through which these two transmitters interact is not well understood. The subsequent doctoral work examines the role of norepinephrine in the regulation of locomotor hyperactivity. The research is on the forefront of expanding our knowledge of catecholaminergic regulation of motor activity, which may lead to development of better pharmacological treatments for hyperactivity disorders. We have identified the mouse mutant coloboma as an animal model for examining the neurological basis of hyperactivity with a well-defined genetic abnormality; these mice carry a mutation that includes the Snap gene. The mouse mutant exhibits spontaneous locomotor hyperactivity that is on average 3 times greater than control mice; this hyperactivity is a direct result of a reduction in SNAP-25 protein and occurs naturally without physical or chemical induction. Administration of
Capsule for the electronic identification of ruminants of any age and weight.

Capsule for the electronic identification of ruminants of any age and weight. Capsule (1) for electronic identification of ruminants, adapted to be administered orally and adapted to be received in the second stomach of the animal, comprising a body (2), of ceramic material and provided with a cavity (3) for enclose a data exchange device (4), it characterized in that it comprises a compound of a non-ferrous element density equal to or greater than 4 g / cm 3} {; It has a specific gravity greater than 3; a total weight comprised between 8 g and 90 g; effective weight between 5 and 85 g; and has an oblong shape into a cylinder with a ratio between length and diameter ranging between 3 and 6. The capsule (1) object of the invention is applicable to animals of different weights and measures.
Field trapping of the adult red stripe weevil, Rhynchophorus vulneratus (Panzer) with an aggregation pheromone in a coconut ecosystem.

Studies were conducted to evaluate a commercially available male produced aggregation pheromone (Ferrugi-on ® ; 4-methyl-5-nonanol), as a monitoring tool for the red stripe palm weevil (RSPW), Rhynchophorus vulneratus Panzer (Coleoptera: Curculionidae) in the coconut ecosystem. The study on pheromone placement, comparing locating the traps at ground level with aerial trapping showed that the mean weekly weevil capture between the two techniques was not statistically significant (F: 0.4955; P = 0.4930). However, catches were numerically higher in the ground trap (mean ± S.D = 3.25 ± 3.77) compared to the aerial trap (mean ± S.D.= 2.25 ± 1.39). Upon sexing of the weevils, there were more females caught, irrespective of location. The male: female ratio over the trapping period was 8:10 and 7:19 respectively for the aerial and ground traps. Irrespective of sex, trap catches peaked in week 3 in the ground trap whereas the aerial trap peaked a week later. Study on adding sugarcane as a complementary bait showed the combination pheromone + kairomone significantly enhanced trap catches. However sugarcane or water alone, or their combination will not trap any weevil. The field trap data showed weevil catches were obtained almost every week suggesting the perennial presence of weevil. The pheromone traps caught a total of 348 adults. The fluctuation in trap catches was significant, with catches of more than 30 weevils recorded for some traps. The findings suggest aggregation pheromone trapping can be a useful monitoring tool for RSPW in Malaysia.
The potential of genomic‐assisted breeding to improve Fusarium head blight resistance in winter durum wheat

Durum wheat is the most important tetraploid wheat mainly used for semolina and pasta production, but is notorious for its high susceptibility to Fusarium head blight (FHB). Our objectives were to identify and characterize quantitative trait loci (QTL) in winter durum and to evaluate the potential of genomic approaches for the improvement of FHB resistance. Here, we employed an international panel of 170 winter and 14 spring durum lines, phenotyped for Fusarium culmorum resistance at five environments. Heading date, plant height and mean FHB severity showed significant genotypic variation with high heritabilities and FHB resistance was negatively correlated with both heading date and plant height. The dwarfing gene Rht-B1 significantly affected FHB resistance and the genome-wide association scan identified eight additional QTL affecting FHB resistance, explaining between 1% and 14% of the genotypic variation. A genome-wide prediction approach yielded only a slightly improved predictive ability compared to marker-assisted selection based on the four strongest QTL. In conclusion, FHB resistance in durum wheat is a highly quantitative trait and in breeding programmes may best be tackled by classical high-throughput recurrent phenotypic selection that can be assisted by genomic prediction if marker profiles are available.
Comparing the sampling performance of sound recorders versus point counts in bird surveys: A meta‐analysis

Abstract Autonomous sound recording is a promising sampling method for birds and other vocalizing terrestrial wildlife. However, while there are clear advantages of passive acoustic monitoring methods over classical point counts conducted by humans, it has been difficult to quantitatively assess how they compare in their sampling performance. Quantitative comparisons of species richness between acoustic recorders and human point counts in bird surveys have previously been hampered by the differing and often unknown detection ranges or sound detection spaces among sampling methods. We performed two meta-analyses based on 28 studies where bird point counts were paired with sound recordings at the same sampling sites. We compared alpha and gamma richness estimated by both survey methods after equalizing their effective detection ranges. We further assessed the influence of technical sound recording specifications (microphone signal-to-noise ratio, height and number) on the bird sampling performance of sound recorders compared to unlimited radius point counts. We show that after standardizing detection ranges, alpha and gamma richness from both methods are statistically indistinguishable, while there might be an avoidance effect in point counts. Furthermore, we show that microphone signal-to-noise ratio (a measure of its quality), height and number positively affect performance through increasing the detection range, allowing sound recorders to match the performance of human point counts. Synthesis and applications. We demonstrate that when used properly, high-end sound recording systems can sample terrestrial wildlife just as well as human observers conducting point counts. Correspondingly, we suggest a first standard methodology for sampling birds with autonomous sound recorders to obtain results comparable to point counts and enable practical sampling. We also give recommendations for carrying out effective surveys and making the most out of autonomous sound recorders.