Miracle-dz/UniFAR-FTUs huggingface dataset:
The roots of the drought: Hydrology and water uptake strategies mediate forest‐wide demographic response to precipitation

Drought‐induced tree mortality is expected to increase globally due to climate change, with profound implications for forest composition, function and global climate feedbacks. How drought is experienced by different species is thought to depend fundamentally on where they access water vertically below‐ground, but this remains untracked so far due to the difficulty of measuring water availability at depths at which plants access water (few to several tens of metres), the broad temporal scales at which droughts at those depths unfold (seasonal to decadal), and the difficulty in linking these patterns to forest‐wide species‐specific demographic responses. We address this problem through a new eco‐hydrological framework: we used a hydrological model to estimate below‐ground water availability by depth over a period of two decades that included a multi‐year drought. Given this water availability scenario and 20 year long‐records of species‐specific growth patterns, we inversely estimated the relative depths at which 12 common species in the forest accessed water via a model of water stress. Finally, we tested whether our estimates of species relative uptake depths predicted mortality in the multi‐year drought. The hydrological model revealed clear below‐ground niches as precipitation was decoupled from water availability by depth at multi‐annual scale. Species partitioned the hydrological niche by diverging in their uptake depths and so in the same forest stand, different species experienced very different drought patterns, resulting in clear differences in species‐specific growth. Finally, species relative water uptake depths predicted species mortality patterns after the multi‐year drought. Species that our method ranked as relying on deeper water were the ones that had suffered from greater mortality, as the zone from which they access water took longer to recharge after depletion. Synthesis. This research changes our understanding of how hydrological niches operate for trees, with a trade‐off between realized growth potential and survival under drought with decadal scale return time. The eco‐hydrological framework highlights the importance of species‐specific below‐ground strategies in predicting forest response to drought. Applying this framework more broadly may help us better understand species coexistence in diverse forest communities and improve mechanistic predictions of forests productivity and compositional change under future climate.
Structure, function and evolution of seryl-tRNA synthetases

Seryl-tRNA synthetase (SerRS) plays the essential role in all organisms of aminoacylating cognate tRNASer with serine. There are four particularly interesting aspects of the serine system. Firstly the existence of six serine codons in two distinct codon groups implies that there is no consistent anti-codon nucleotide in tRNASers. Perhaps because of this, SerRS is one of the very few synthetases that does not specifically recognize the anticodon. Secondly, with the exception of mammalian mitochondria, all tRNASers are class 2 tRNAs, that is they possess a long variable arm. This feature is the major identity element of tRNASer and SerRS has acquired a unique feature to recognize it, an N-terminal coiled-coil domain. Exactly how the highly unusual mammalian mitochondria tRNASers are recognized by mitochondrial seryl-tRNA synthetase is still unclear. Thirdly, the majority of organisms require co-translational incorporation of seleno-cysteine (Sec) into a few critical seleno-proteins. This is achieved by SerRS firstly charging a specialized and unique suppressor tRNA, tRNASec with serine and subsequently enzymatic conversion of Ser-tRNASec to Sec-tRNASec. The latter species can be used to incorporate seleno-cysteine at stop codons in seleno-proteins by means of a special mechanism that depends on the codon context. Fourthly, although in general SerRSs are universally rather well conserved enzymes, it has recently been discovered that a form with a markedly diverged primary sequence exists in a limited group of archeabacteria. The reason for this is still obscure. In this chapter we review what is known about SerRS structure and function and the co-evolution of SerRS and tRNASer and their mode of recognition in different organisms.
Large-scale neuroimaging and genetic study reveals genetic architecture of brain white matter microstructure

Microstructural changes of white matter (WM) tracts are known to be associated with various neuropsychiatric disorders/diseases. Heritability of structural changes of WM tracts has been examined using diffusion tensor imaging (DTI) in family-based studies for different age groups. The availability of genetic and DTI data from recent large population-based studies offers opportunity to further improve our understanding of genetic contributions. Here, we analyzed the genetic architecture of WM tracts using DTI and single-nucleotide polymorphism (SNP) data of unrelated individuals in the UK Biobank (n ∼ 8000). The DTI parameters were generated using the ENIGMA-DTI pipeline. We found that DTI parameters are substantially heritable on most WM tracts. We observed a highly polygenic or omnigenic architecture of genetic influence across the genome as well as the enrichment of SNPs in active chromatin regions. Our bivariate analyses showed strong genetic correlations for several pairs of WM tracts as well as pairs of DTI parameters. We performed voxel-based analysis to illustrate the pattern of genetic effects on selected parts of the tract-based spatial statistics skeleton. Comparing the estimates from the UK Biobank to those from small population-based studies, we illustrated that sufficiently large sample size is essential for genetic architecture discovery in imaging genetics. We confirmed this finding with a simulation study.
Storage of Hatching Eggs : Effects of storage and early incubation conditions on egg characteristics, embryonic development, hatchability, and chicken quality

Key words: egg storage, embryonic development, albumen quality, hatchability, chick quality It is well known that an increase in the storage duration increases incubation duration and decreases hatchability and chick quality. The negative effects of prolonged egg storage (> 7 days) may be caused by changes in the embryo, in the egg characteristics, or by both. The first aim of the current thesis was to investigate which physiological mechanisms are involved in the negative effects of prolonged egg storage on hatchability and chick quality. The second aim was to investigate how these negative effects of prolonged egg storage can be reduced by making changes in storage or early incubation conditions. Treatments, such as prestorage incubation, frequent warming during storage, a change in the storage air composition, different preincubation warming profiles, and hypercapnic incubation during the first 5 days of incubation were used in the current thesis to gain more insight in the cause of the negative effects of prolonged egg storage. Prestorage incubation and frequent warming during storage increased the stage of embryonic development and the number of viable embryonic cells. The effect of these treatments on hatchability was nihil, positive or negative and seems to depend on the stage of embryonic development before and after the treatment. The storage air compositions, studied in the current thesis did not affect embryonic development, hatchability, or chick quality, when eggs were stored for 14 days. This suggests that changes in albumen quality during storage do not affect hatchability and chick quality. The 24-h preincubation warming profile decreased embryonic mortality during the first 9 days of incubation in comparison with the 4-h preincubation warming profile when eggs were stored for 13 days. Hypercapnic incubation during the first 5 days of incubation decreased albumen pH during early incubation, but did not improve hatchability. In conclusion, embryo characteristics seem to have a more important role in the negative effects of prolonged egg storage than changes in the egg characteristics, such as changes in the albumen pH and albumen height.
Spatial distribution of total and bioavailable heavy metal contents in soil from agricultural, residential, and industrial areas in Sudan

Abstract The current work aims at determining and assessing the total and bioavailable concentrations of some heavy metals, besides some properties, in soil samples from agricultural, industrial, and residential areas in Sudan. The GIS maps show similar trend of all examined metals in Marawi (the Northern state) area and different trends in other areas. Cluster analysis of the total contents of heavy metals shows the classification of 18 locations in Alhasahisa area in one group while the rest of locations from the three examined areas scattered in other nine groups with high variations.
A re-evaluation of subtidal Lithophyllum species (Corallinales, Rhodophyta) from North Carolina, USA, and the proposal of L. searlesii sp. nov.

Abstract: The current identification of crustose coralline algae from North Carolina is based on a few morphoanatomical studies from the last century. We reassessed the type specimens of the two Lithophyllum species historically reported from offshore communities in North Carolina, L. intermedium with a Caribbean Sea type locality and L. subtenellum with an Atlantic southern France type locality, using scanning electron microscopy images and diagnostic rbcL sequences. Neither of the sequences generated from the type specimens matched rbcL sequences from contemporary specimens collected from subtidal North Carolina epibenthic communities. On the basis of analyses of rbcL and other loci (psbA, UPA, and COI), we instead found L. atlanticum, recently described from Brazil, and L. searlesii sp. nov. from Onslow Bay, North Carolina. These sequence data show that L. atlanticum is related to northeast Pacific species, whereas L. searlesii is related to Mediterranean species.
Morphometric variations between triploid and diploid Clarias gariepinus (Burchell, 1822)

Abstract Several scientific methods have been described in the identification of triploid fish. However, many of these methods are not applicable for routine management purposes due to their complexity and cost. In this study, the possibility of using morphological variation as a least cost and less complex method of distinguishing triploid and diploid African catfish Clarias gariepinus (Burchell, 1822) was examined. Triploid catfish were produced by cold shock of fertilized eggs in 5°C for 20 mins (at approximately 3 mins after fertilization). The fish were incubated, hatched and raised for 3 months. Ploidy levels of the fish were then ascertained by observing the erythrocyte shape. Triploid erythrocyte was ellipsoidal in shape while diploid was round. Morphological characterization was then carried out on 100 samples each of triploid and diploid African catfish. Although significant differences were observed in many parameters, the principal morphometric difference between triploid and diploid African catfish could not be clearly distinguished. It was therefore concluded that morphological characteristics is not ideal for discriminating triploids and diploids of African catfish. The used of erythrocyte characteristics still remains the cheapest and relatively effective method for triploid and diploid determination in African catfish.
The world fauna of Synchroidae Lacordaire, 1859 (Coleoptera, Tenebrionoidea, Synchroidae)

Synchroidae Lacordaire, 1859 is a taxonomically and biologically poorly known group. In the present paper, diagnostic characters used to separate genera are analysed and the phylogenetic relationships within this family are preliminarily investigated. Results suggest that the characteristic Synchroa pangu Hsiao, Li, Liu & Pang, 2016 can be removed to establish a new genus, Thescelosynchroa gen. nov. The new combination, T. pangu (Hsiao, Li, Liu & Pang) gen. et comb. nov., is proposed. The definitions of Synchroa Newman, 1838 and Synchroina Fairmaire, 1898 are revised. Moreover, morphological analysis and character comparison also suggest that the familial placement of Mallodrya subaenea Horn, 1888 is questionable. Six species are re-examined and re-diagnosed: Synchroa chinensis Nikitsky, 1999, S. elongatula Nikitsky, 1999, S. formosana Hsiao, 2015, S. melanotoides Lewis, 1895, S. punctata Newman, 1838 and Synchroina tenuipennis Fairmaire, 1898. The male of S. chinensis and the female of S. formosana are described for the first time. Synchroa elongatula and Synchroina tenuipennis are newly recorded from Laos and Indonesia, respectively. We also hypothesize that the Eastern Asian-North American disjunction of Synchroa could be connected to a Mid-Late Tertiary migration of plants via the Bering Land Bridge.
Recreating bioenergetic elements in protein maquettes

In all organisms, protein-mediated electron transfers underlie energy metabolism and countless other critical metabolic pathways. Deciphering the factors governing electron transfers offers enormous practical value, including finding reliable guidelines for metabolic engineering to produce clean solar fuels. Protein maquettes provide simple, flexible scaffolds to study biological electron transfer processes. The maquette approach to protein design builds man-made oxidoreductases from first principles with minimal reference to natural protein sequences. This scheme has produced impressive in vitro and in vivo results to replicate the functions of natural oxidoreductases using simple, straightforward α-helical bundles. The redox function of maquettes has so far been limited to electron transfers within a single water-soluble molecule. This work extends the maquette project to examine electron transfers A) between diffusing redox partners and B) in amphiphilic proteins. Nature employs complimentary electrostatic surfaces to bring diffusing redox proteins together, and a series of maquettes of varying surface charge demonstrate that the same principles apply to flexible manmade proteins. A heme-binding maquette of complimentary surface charge is shown to reduce natural cytochrome c at physiological rates, while a maquette variant similar in charge to cyt c shows a far weaker interaction. The ionic strength dependence of these interactions is shown to be broadly similar to that in natural proteins. This work also presents the first intra-protein redox function in a de novo amphiphilic protein and describes progress toward transmembrane electron transfer analogous to that in the cytochrome bc1 complex. These functional achievements are remarkable given that the proteins are designed from first principles without atomically resolved structures, and they hold promise for future efforts in applying artificial proteins to new metabolic pathways. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Biochemistry & Molecular Biophysics First Advisor Peter L. Dutton Second Advisor Bohdana M. Discher
Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes

Rahemi, A. , Gradziel T.M. , Chaparro J.X. , Folta, K.M. , Taghavi, T. , Fatahi, R. , Ebadi, A. and Hassani, D. 2015. Phylogenetic relationships among the first and second introns of selected Prunus S-RNase genes. Can. J. Plant Sci. 95: 1145-1154. To identify and evaluate self-incompatible alleles in almonds and related germplasm, DNA from 15 Prunus species was amplified using two degenerate consensus primer pairs flanking first and second S-locus introns (PaConsI-FD+EM-Pc1ConsRD and EM-Pc2ConsFD+EM-Pc3ConsRD). Twenty-eight amplified PCR products were analyzed by automated sequencer capillary electrophoresis. Sequenced fragments were aligned against available Prunus S-locus sequences in the National Center for Biotechnology Information and S-alleles identities were determined. The phylogenetic relationships between S-alleles in the germplasm studied were determined by the homology between their sequences and dendrograms were obtained for each primer pair. The Maximum Likelihood (homology) ranged from 84 to 100%. Most sequences were similar to cultivated almond (Prunus dulcis) or to the European wild almond (P. webbii). Twenty-six alleles for the first and the second introns were registered in the database in the GenBank. Two sequences of the first and second introns, which were taken from Prunus nairica and had similarity in GenBank, were registered in the database under a common sequence of the first and second intron. Analysis of phylogenetic relationships (dendrograms) among S-alleles from wild almond species as well as S-alleles cluster relations showed most pairs of alleles well supported by bootstrap.
Bacterial Innate Immunity: Mechanisms of PhoQ Sensing that Promote Salmonella Virulence

Bacterial Innate Immunity: Mechanisms of PhoQ Sensing that Promote Salmonella Virulence Kevin George Hicks Chair of the Supervisory Committee: Samuel I. Miller Department of Microbiology, Genome Sciences, and Medicine Salmonella PhoQ is a histidine kinase with a periplasmic sensor domain that promotes virulence by detecting the hostile environment of the host macrophage phagosome. PhoQ kinase activity is repressed by divalent cations and induced in environments of acidic pH, limited divalent cations, and cationic antimicrobial peptides (CAMP). Upon activation, PhoQ phosphorylates the response regulator PhoP, coordinating regulation of greater than three hundred genes involved in virulence and intracellular survival. Previously, it was unclear which host signals are sensed by salmonellae to promote PhoPQ-mediated virulence. Using NMR and random activating mutagenesis, we defined conformational changes produced in the PhoQ periplasmic domain on exposure to acidic pH that indicate structural flexibility is induced in αhelices 4 and 5, suggesting this region contributes to sensing fluctuations in periplasmic pH. Therefore, we engineered a disulfide bond between the residues W104C and A128C in the PhoQ periplasmic domain that restrains conformational flexibility between the α-helices 4 and 5 and the α/β-core of the periplasmic domain. PhoQ is responsive to CAMP, but is inhibited for activation by acidic pH and divalent cation limitation. Salmonella enterica Typhimurium with the phoQ allele are virulent in mice and macrophages, indicating that acidic pH and divalent cation sensing by PhoQ are dispensable for virulence.
A cross‐continental comparison of assemblages of seed‐ and fruit‐feeding insects in tropical rain forests: Faunal composition and rates of attack

Insects feeding on seeds and fruits represent interesting study systems, potentially able to lower the fitness of their host plants. In addition to true seed eaters, a suite of insects feed on the fleshy parts of fruits. We examined the likelihood of community convergence in whole insect assemblages attacking seeds/fruits in three tropical rain forests.
Evaluasi Ketahanan Galur International Rice Bacterial Blight terhadap Hawar Daun Bakteri dan Identifikasi Patotipe Xanthomonas oryzae pv. oryzae Provinsi Jawa Tengah Berdasarkan Galur IRBB

Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae ( Xoo ) is the major disease in rice plants causing considerable economic losses. The objective of the study was to evaluate the resistant International Rice Bacterial Blight (IRBB) lines against bacterial leaf blight and the identification of Xoo pathotype from Central Java Province as the basis recommendation of the resistant varieties assembly with the background of resistant genes to overcome BLB disease. The evaluation of Xoo isolates from 22 districts in Central Java Province on IRBB lines was conducted in the rainy season 2016-2017 using split plot with three replications. The main plot was 15 IRBB lines, while the subplot was 110 Xoo isolates. Among 15 lines of IRBB, there were 10 lines have functioned as pathotype examiner of Xoo . The results obtained 6 lines were reacted resistant, namely IRBB5, IRBB7, IRBB8, IRBB57, IRBB64, and IRBB66. The IRBB66 line can be used as a resistant elder for the assembly of BLB resistant varieties because it has a combination of pyramiding resistant genes that were effective against BLB in some areas of Central Java Province. Pathotype IX was only found and dominant in Pemalang. Pathotype X was obtained in six districts of Tegal, Brebes, Banjarnegara, Purbalingga, Purworejo, and Grobogan. Pathotype XII was the most dominant prototype in 15 districts. Assembling of resistant varieties with resistant gene backgrounds based on the existence of a specific Xoo pathotype in the field can reduce the severity of BLB disease.
The role of the serotonin transporter gene, brain structure and family environment in the emergence of depression during adolescence

Recent findings suggest that complex interrelations between genetics, brain structure and environmental contexts, including stressors and family processes, may have a role in the development of depressive disorders. The role of a functional variant in the 5-HT transporter promoter region polymorphism (5-HTTLPR) and its potential interaction with adverse, stressful life events in predicting depression has been the focus of considerable research attention. The validity of this gene-environment interaction, however, has been queried due to inconsistent findings. The current thesis aims to enhance current understanding of this interaction by considering how two different dimensions of environmental experience (threat versus deprivation) might interact with the serotonin transporter gene during adolescence, while also investigating potential underlying neurobiological mechanisms. Three interconnected studies were conducted that examined the interplay between the serotonin transporter gene, family environment, brain regions of interest and depression. Study 1 examined whether 5-HTTLPR moderated associations between (1) high levels of negative, harsh, critical parenting behaviours (as an index of more threatening environments) and subsequent depression and (2) low levels of positive, supportive parenting behaviours (as an index of more deprived environments) and subsequent depression during adolescence. These GxE interactions were tested in adolescents from two independent longitudinal studies, the Australian Temperament Study (ATP, n=681) a population based sample that relied on questionnaire measures of environment and depression, and the Orygen Adolescent Development Study (ADS, n=174) a sample