Standard name
Human Ortholog
Description Protein with an N-terminal kelch-like domain; putative negative regulator of early meiotic gene expression; required, with Mds3p, for growth under alkaline conditions; PMD1 has a paralog, MDS3, that arose from the whole genome duplication
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Micrographs

ensLOC DeepLoc
Localization WT1 WT2 WT3 RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3 WT1 WT2 WT3 AF100 AF140 AF180
Cortical Patches 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud Neck 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud Site 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 – – – – – –
Cell Periphery 0.07 0 0 0 0 0 0 0 0.05 – 0.05 0.06 0 0 0 0 0 0 0 0 0 0 0 0
Cytoplasm 0.97 0.98 0.99 0.99 0.97 0.93 0.9 0.84 0.8 – 0.72 0.75 1.0 1.0 0.98 0.96 0.94 0.94 0.96 0.92 0.93 0.93 0.94 0.92
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Endosome 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Golgi 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Mitochondria 0 0 0 0.08 0.06 0.2 0.22 0.24 0.38 – 0.47 0.41 0 0 0 0 0 0 0 0 0 0 0 0
Nucleus 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Nuclear Periphery 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Nucleolus 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Peroxisomes 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SpindlePole 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Vac/Vac Membrane 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0.06 0.05 0 0 0 0 0 0
ensLOC DeepLoc
Localization WT1 WT2 WT3 RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3 WT1 WT2 WT3 AF100 AF140 AF180
Cortical Patches 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 1 0 1 0 0 0 2
Bud 0 0 6 5 0 5 0 6 3 – 7 5 2 0 3 0 0 1 0 1 0 1 1 1
Bud Neck 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 1 0 0 0 1
Bud Site 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 – – – – – –
Cell Periphery 30 4 6 11 9 11 17 9 21 – 13 22 6 2 5 12 38 34 0 0 0 0 1 0
Cytoplasm 442 239 300 310 349 386 441 423 340 – 185 255 251 308 268 526 841 906 442 222 277 149 299 279
Endoplasmic Reticulum 0 2 0 0 3 0 1 0 0 – 3 3 0 1 2 11 22 26 2 1 5 0 4 4
Endosome 3 1 0 0 2 1 0 1 0 – 0 1 0 0 0 2 1 2 3 2 1 1 1 1
Golgi 0 0 0 0 0 0 0 1 0 – 0 0 0 0 0 0 2 0 1 1 2 0 0 1
Mitochondria 5 2 5 25 23 85 106 123 163 – 121 139 0 2 10 7 7 10 4 2 6 2 2 2
Nucleus 2 1 0 1 2 0 1 5 2 – 0 1 0 0 0 12 16 12 0 1 0 1 0 0
Nuclear Periphery 1 0 0 0 0 0 0 1 0 – 1 1 0 0 0 0 0 0 0 0 0 0 0 0
Nucleolus 1 0 0 0 0 1 0 2 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Peroxisomes 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 1 0 0 0 0 0 0 0
SpindlePole 0 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 1 0 0 0 0 0
Vac/Vac Membrane 12 0 2 2 3 1 6 7 5 – 9 5 0 0 0 17 52 51 1 4 1 0 2 3
Unique Cell Count 456 244 303 312 360 415 490 503 425 258 339 251 309 273 546 897 966 463 243 299 161 319 303
Labelled Cell Count 496 249 319 354 391 490 572 578 534 339 432 259 313 288 587 980 1043 463 243 299 161 319 303


Cytoplasm

(Huh et al. Nature 2003 425:686)
Screen WT1 WT2 WT3 RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3 AF100 AF140 AF180
Mean Cell GFP Intensity (1e-4) 7.4 5.9 5.4 5.3 5.7 5.1 5.0 5.1 4.6 – 4.5 4.5 6.6 6.3 5.5 8.8 9.9 9.2 6.3 6.4 7.7
Std Deviation (1e-4) 1.4 1.1 1.1 1.3 1.3 1.2 1.2 1.4 1.0 – 1.1 1.3 1.2 1.1 1.0 1.7 2.2 1.6 1.4 1.4 1.6
Intensity Change (Log2) – – – -0.02 0.1 -0.08 -0.11 -0.08 -0.22 – -0.26 -0.26 0.29 0.23 0.05 0.71 0.89 0.78 0.24 0.26 0.53


Localization RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3
Cortical Patches 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0
Bud -0.4 0 0 0 0 0 – 0 0 0 0 0 0 0 0
Bud Neck 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0
Bud Site 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0
Cell Periphery 1.2 0.4 0.6 1.2 -0.2 0 – 0 0 0.3 0 -0.1 0.2 1.8 1.3
Cytoplasm 0.5 -1.8 -3.8 -5.0 -6.7 -7.8 – -9.4 -8.8 1.6 1.0 -0.9 -2.3 -3.7 -3.7
Endoplasmic Reticulum 0 0 0 0 0 0 – 0 0 0 0 0 0 2.8 2.9
Endosome 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0
Golgi 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0
Mitochondria 3.7 3.0 7.5 7.9 8.6 0 – 0 0 0 0 1.5 0 0 0
Nucleus 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0
Nuclear Periphery 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0
Nucleolus 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0
Peroxisomes 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0
SpindlePole 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0
Vacuole 0 0 0 0 0 0 – 2.4 0 0 0 0 2.3 3.7 3.5

Images

Circle plot not available

Protein Concentration and Protein Localization Data

R1 R2 R3
G1 Pre-START G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Pre-START G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Pre-START G1 Post-START S/G2 Metaphase Anaphase Telophase
Concentration 4.8654 5.2833 4.793 4.2265 4.2242 4.6533 2.5972 4.951 4.3682 3.9274 3.8403 4.3935 4.6004 6.2036 5.0861 5.2409 5.3746 5.2677
Actin 0.0243 0.0008 0.0246 0.0112 0.0012 0.0006 0.0024 0.0003 0.0014 0.0076 0.0013 0.01 0.0346 0.0039 0.0041 0.0013 0.012 0.0016
Bud 0.0016 0.0002 0.0033 0.0021 0.0004 0.0001 0.0003 0.0001 0.0082 0.0013 0.0002 0.0002 0.0008 0.0021 0.0008 0.0006 0.0012 0.0031
Bud Neck 0.0049 0.0003 0.0017 0.0027 0.0005 0.0009 0.0027 0.0001 0.0002 0.0127 0.0003 0.0024 0.0016 0.0006 0.0007 0.0004 0.0005 0.0013
Bud Periphery 0.002 0.0002 0.0017 0.0064 0.0002 0.0001 0.0002 0.0001 0.0034 0.0022 0.0002 0.0001 0.0011 0.0015 0.001 0.0013 0.0014 0.0028
Bud Site 0.0237 0.0033 0.0115 0.0033 0.0032 0.0001 0.0009 0.0026 0.001 0.0097 0.0007 0.0003 0.0021 0.0229 0.0043 0.001 0.0018 0.0005
Cell Periphery 0.0021 0.0028 0.0023 0.004 0.0003 0.0002 0.0002 0.0003 0.0003 0.0007 0.0001 0 0.0008 0.0011 0.0006 0.0006 0.0004 0.0002
Cytoplasm 0.5924 0.8419 0.8636 0.8073 0.8456 0.9432 0.527 0.8289 0.8131 0.8842 0.7816 0.8768 0.6072 0.8358 0.778 0.8077 0.7719 0.852
Cytoplasmic Foci 0.0103 0.0036 0.003 0.006 0.0226 0.0028 0.0478 0.002 0.0046 0.0052 0.0302 0.0226 0.0555 0.0153 0.0141 0.0202 0.0079 0.004
Eisosomes 0.0002 0.0001 0.0002 0.0004 0 0 0 0 0 0.0001 0 0 0.0004 0.0001 0.0001 0.0001 0.0003 0
Endoplasmic Reticulum 0.0138 0.0052 0.0085 0.0091 0.0027 0.0045 0.0104 0.0059 0.0018 0.0023 0.0054 0.0039 0.0061 0.0033 0.0033 0.0043 0.0019 0.0015
Endosome 0.0136 0.0076 0.0028 0.0219 0.0057 0.0014 0.0655 0.003 0.0009 0.0059 0.0035 0.01 0.0383 0.0025 0.0092 0.0363 0.0017 0.0013
Golgi 0.0026 0.0014 0.001 0.0021 0.0004 0.0002 0.0044 0.0004 0.0002 0.0024 0.0026 0.0058 0.0183 0.0006 0.0075 0.015 0.0008 0.0003
Lipid Particles 0.0016 0.0003 0.0006 0.0012 0.0011 0.0001 0.0026 0.0006 0.0001 0.0007 0.0086 0.0005 0.0061 0.0008 0.0011 0.0073 0.0003 0.0001
Mitochondria 0.002 0.0003 0.0003 0.004 0.002 0.0001 0.0009 0.0001 0.0148 0.0007 0.0003 0.001 0.0029 0.0002 0.009 0.0048 0.0003 0.0001
None 0.2582 0.122 0.0667 0.079 0.0358 0.0438 0.2979 0.1538 0.1475 0.0585 0.1213 0.062 0.1864 0.1039 0.1587 0.0849 0.1939 0.1289
Nuclear Periphery 0.0176 0.004 0.0044 0.0114 0.0545 0.0003 0.0058 0.0004 0.0003 0.0004 0.0006 0.0005 0.0009 0.0008 0.0006 0.001 0.0005 0.0003
Nucleolus 0.0014 0.0001 0.0001 0.0006 0.0038 0 0.0008 0 0.0001 0.0002 0.0001 0 0.0002 0.0002 0.0001 0.0005 0.0001 0
Nucleus 0.014 0.0029 0.0016 0.0061 0.009 0.0007 0.0179 0.0004 0.0007 0.0011 0.0008 0.0006 0.001 0.0011 0.0011 0.0013 0.0008 0.0009
Peroxisomes 0.001 0 0.0001 0.0005 0.0002 0 0.0013 0 0.0001 0.0011 0.0353 0.0021 0.0322 0.0006 0.0033 0.0032 0.0005 0.0001
Punctate Nuclear 0.0059 0.0004 0.0007 0.0013 0.0049 0.0001 0.0049 0.0002 0.0003 0.0002 0.0061 0.0006 0.0016 0.0018 0.0005 0.0005 0.0013 0.0006
Vacuole 0.0058 0.0024 0.0013 0.0156 0.0034 0.0005 0.0055 0.0005 0.0009 0.0024 0.0006 0.0003 0.0017 0.0009 0.0016 0.0068 0.0006 0.0003
Vacuole Periphery 0.0011 0.0003 0.0002 0.0039 0.0025 0.0001 0.0007 0.0001 0.0001 0.0003 0.0001 0.0001 0.0004 0.0001 0.0004 0.001 0.0001 0.0001

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 16.6706 12.7468 15.9963 16.7291 12.6422 16.1374 17.5792 16.7578 12.6871 19.2866
Translational Efficiency 0.2486 0.3888 0.2607 0.1758 0.2444 0.2763 0.2386 0.1622 0.2499 0.2178

Hit Data

Dataset Hit
Protein Concentration ✘
Protein Localization ✘
Gene Expression ✘
Translational Efficiency ✘

Micrographs

Cell Count

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
212 163 552 987 1161 2078 457 111 1373 2241 1009 1098

Protein Abundance

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Mean 728.34 857.58 1280.55 840.65 752.19 831.64 957.29 1004.58 748.51 833.53 1134.14 857.22
Standard Deviation 107.57 113.37 184.96 117.77 106.33 110.17 166.51 134.39 106.87 110.61 239.10 129.37
Intensity Change Log 2 — 0.235659 0.814080 0.206893 — 0.144862 0.347859 0.417423 — 0.190244 0.595993 0.317687

Localization Score (DeepLoc)

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Actin 0.000196 0.000377 0.000512 0.000331 0.000287 0.000563 0.000066 0.002224 0.000273 0.000549 0.000310 0.000522
Bud Neck 0.008934 0.010072 0.001749 0.010967 0.005194 0.014176 0.001703 0.002878 0.005771 0.013877 0.001728 0.010149
Bud Site 0.013093 0.017664 0.005960 0.023294 0.006206 0.016487 0.004023 0.055535 0.007269 0.016573 0.005082 0.026554
Cell Periphery 0.000412 0.000134 0.000158 0.000274 0.000134 0.000131 0.000325 0.000303 0.000177 0.000131 0.000234 0.000277
Cytoplasm 0.632781* 0.498823* 0.637666* 0.466915* 0.636236* 0.641037* 0.543366* 0.437421* 0.635702* 0.630693* 0.594955* 0.463933*
Cytoplasmic Foci 0.159887 0.225831* 0.020132 0.050138 0.151996 0.172031 0.051185 0.058637 0.153214 0.175944 0.034197 0.050997
Eisosomes 0.000144 0.000089 0.000022 0.000114 0.000082 0.000139 0.000127 0.000065 0.000092 0.000135 0.000070 0.000109
Endoplasmic Reticulum 0.002567 0.000919 0.001565 0.001274 0.001569 0.000828 0.000540 0.001604 0.001723 0.000835 0.001101 0.001307
Endosome 0.004402 0.029142 0.002264 0.018541 0.008632 0.013967 0.003334 0.007101 0.007979 0.015070 0.002749 0.017384
Golgi 0.001020 0.001990 0.000163 0.003306 0.000819 0.004154 0.000080 0.001574 0.000850 0.003996 0.000125 0.003131
Lipid Particles 0.002838 0.001904 0.001124 0.005986 0.002496 0.001738 0.002442 0.001839 0.002549 0.001750 0.001721 0.005567
Mitochondria 0.001205 0.000328 0.000202 0.008798 0.001226 0.003002 0.000180 0.030443 0.001223 0.002807 0.000192 0.010986
Mitotic Spindle 0.000115 0.001159 0.002330 0.015616 0.001786 0.004175 0.001908 0.069086 0.001528 0.003956 0.002139 0.021021
None 0.001397 0.000334 0.007517 0.007269 0.001568 0.000604 0.009321 0.002521 0.001541 0.000585 0.008334 0.006789
Nuclear Periphery 0.000274 0.000168 0.000585 0.000444 0.000249 0.000108 0.000542 0.000328 0.000253 0.000113 0.000565 0.000432
Nuclear Periphery Foci 0.000610 0.002178 0.004781 0.001291 0.000840 0.000329 0.000829 0.005202 0.000804 0.000463 0.002991 0.001686
Nucleolus 0.000327 0.001483 0.000124 0.001813 0.000316 0.000284 0.000572 0.000114 0.000318 0.000371 0.000327 0.001641
Nucleus 0.109655 0.044546 0.211927* 0.128036 0.102963 0.041708 0.248861* 0.034594 0.103996 0.041914 0.228655* 0.118589
Peroxisomes 0.001098 0.008733 0.000146 0.005634 0.001648 0.003551 0.000337 0.005624 0.001563 0.003928 0.000232 0.005633
Vacuole 0.058428 0.153419 0.100938 0.246038* 0.075208 0.079111 0.130131 0.259696* 0.072617 0.084516 0.114160 0.247419*
Vacuole Periphery 0.000617 0.000707 0.000134 0.003923 0.000545 0.001877 0.000129 0.023212 0.000556 0.001792 0.000132 0.005873

Localization Changes (T-score)

R1 R2 R1 & R2
UBP2_WT UBP14_WT UBP2UBP14_WT UBP2UBP14_UBP2 UBP2UBP14_UBP14 UBP2_WT UBP14_WT UBP2UBP14_WT UBP2UBP14_UBP2 UBP2UBP14_UBP14 UBP2_WT UBP14_WT UBP2UBP14_WT UBP2UBP14_UBP2 UBP2UBP14_UBP14
Actin -2.97 -6.07 -1.41 1.64 4.80 -2.03 1.47 -1.79 -1.36 -2.01 -2.29 -1.91 -1.09 1.30 0.49
Bud Neck -0.14 2.64 0.54 0.68 -3.43 -8.45 5.68 3.49 10.38 -0.61 -7.74 5.55 -1.05 4.64 -3.71
Bud Site -0.94 1.57 -0.98 -0.02 -3.60 -6.96 0.98 -2.58 -1.50 -2.72 -6.46 0.81 -4.23 -0.76 -4.75
Cell Periphery 2.87 2.09 2.34 -1.99 1.12 0.39 -3.78 -1.71 -1.78 0.25 2.40 -2.22 -0.59 -2.93 1.49
Cytoplasm 4.89 5.58 11.17 3.22 6.81 -0.86 10.23 7.13 7.49 2.03 0.17 11.88 18.43 19.50 6.45
Cytoplasmic Foci -2.89 13.38 11.28 11.21 -7.59 -3.22 20.12 14.48 18.67 -1.22 -3.76 26.84 23.21 31.01 -4.72
Eisosomes 2.64 6.88 3.07 0.21 -9.47 -4.48 -2.16 1.81 5.06 3.18 -3.64 5.64 0.76 3.94 -3.98
Endoplasmic Reticulum 1.76 0.84 1.57 -0.17 1.80 2.25 1.91 0.29 -1.80 -1.32 2.71 1.02 1.54 -0.65 1.06
Endosome -3.91 4.69 -3.66 2.46 -4.68 -4.53 6.04 3.18 6.81 -0.54 -6.15 7.05 -1.61 1.87 -4.55
Golgi -1.42 2.95 -1.30 -0.19 -2.55 -7.77 8.58 1.21 7.45 -1.54 -7.82 8.36 -1.56 2.89 -2.66
Lipid Particles 1.77 2.54 -1.00 -1.91 -2.19 3.99 1.08 1.28 -0.59 0.35 4.46 3.06 -1.27 -2.16 -1.98
Mitochondria 2.38 2.59 -2.50 -3.12 -3.16 -2.21 2.16 -0.99 -0.71 -1.14 -2.18 2.45 -2.66 -1.61 -3.36
Mitotic Spindle -1.67 -5.04 -5.13 -4.72 -3.59 -2.05 -2.20 -2.19 -1.98 -1.65 -2.28 -3.18 -5.08 -4.11 -3.40
None 3.37 -6.93 -2.76 -3.64 0.32 4.88 -3.52 -0.39 -2.72 3.33 5.49 -5.94 -2.71 -3.58 1.15
Nuclear Periphery 1.30 -9.17 -4.44 -8.24 5.73 6.60 -10.43 -2.32 -3.51 3.63 6.57 -16.58 -7.65 -11.08 6.83
Nuclear Periphery Foci -3.31 -10.55 -1.78 1.02 5.93 6.88 -3.54 -3.32 -3.99 -2.53 4.47 -10.63 -1.98 -2.73 3.69
Nucleolus -1.14 3.20 -3.07 0.22 -3.64 0.49 -2.36 6.98 2.74 5.62 -0.60 0.53 -3.04 -2.69 -3.10
Nucleus 5.30 -9.38 0.38 -8.16 13.81 13.59 -10.75 9.12 -0.08 16.01 14.75 -16.46 0.97 -12.94 17.00
Peroxisomes -3.22 8.11 -3.05 1.99 -4.28 -4.33 3.90 -0.25 1.53 -1.57 -5.54 4.59 -2.31 0.72 -4.40
Vacuole -6.24 -9.81 -23.13 -10.31 -11.80 -0.40 -11.96 -10.65 -10.63 -5.27 -2.57 -15.56 -28.94 -28.42 -12.28
Vacuole Periphery -0.32 4.45 -2.49 -2.40 -3.21 -3.20 5.69 -1.00 -0.75 -1.08 -3.20 6.61 -2.62 -1.02 -3.14
Standard name
Human Ortholog
Description Protein with an N-terminal kelch-like domain; putative negative regulator of early meiotic gene expression; required, with Mds3p, for growth under alkaline conditions; PMD1 has a paralog, MDS3, that arose from the whole genome duplication
Localization
Cell Percentages cytoplasm (84%)
Cell Cycle Regulation No
Subcompartmental Group cytoplasm-9

Pmd1

Pmd1


Nearest neighbours ( genes)

correlation threshold

0.6

1.0

0.80


Biological Process (Gene Ontology)
Molecular Function (Gene Ontology)
Cellular Component (Gene Ontology)

Endocytosis
Temp Actin Patch (Sac6-tdTomato) Cortical Patch (Sla1-GFP) Late Endosome (Snf7-GFP) Vacuole (Vph1-GFP)
37℃
RT
Cell Cycle Omics

CYCLoPs (Pmd1-GFP)
Gene / Allele Actin Patch (Sac6-tdTomato) Cortical Patch (Sla1-GFP) Late Endosome (Snf7-GFP) Vacuole (Sac6-tdTomato)
Gene Images
Gene Images
Images are not yet available
Images are not yet available